Arginine methyltransferase inhibitors and uses thereof

ABSTRACT

Described herein are compounds of Formula (I), pharmaceutically acceptable salts thereof, and pharmaceutical compositions thereof. Compounds of the present invention are useful for inhibiting arginine methyltransferase activity. Methods of using the compounds for treating arginine methyltransferase-mediated disorders are also described.

RELATED APPLICATIONS

The present application claims priority under 35 U.S.C. §119(e) to U.S. provisional patent application, U.S. Ser. No. 61/781,063, filed Mar. 14, 2013, the entire contents of which is incorporated herein by reference.

BACKGROUND OF THE INVENTION

Epigenetic regulation of gene expression is an important biological determinant of protein production and cellular differentiation and plays a significant pathogenic role in a number of human diseases.

Epigenetic regulation involves heritable modification of genetic material without changing its nucleotide sequence. Typically, epigenetic regulation is mediated by selective and reversible modification (e.g., methylation) of DNA and proteins (e.g., histones) that control the conformational transition between transcriptionally active and inactive states of chromatin. These covalent modifications can be controlled by enzymes such as methyltransferases (e.g., arginine methyltransferases), many of which are associated with specific genetic alterations that can cause human disease.

Disease-associated chromatin-modifying enzymes (e.g., arginine methyltransferases) play a role in diseases such as proliferative disorders, autoimmune disorders, muscular disorders, vascular disorders, metabolic disorders, and neurological disorders. Thus, there is a need for the development of small molecules that are capable of inhibiting the activity of arginine methyltransferases.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS

Arginine methyltransferases are attractive targets for modulation given their role in the regulation of diverse biological processes. It has now been found that compounds described herein, and pharmaceutically acceptable salts and compositions thereof, are effective as inhibitors of arginine methyltransferases. Such compounds have the general Formula (I):

or a pharmaceutically acceptable salt thereof, wherein R₁, R₃, R_(x), X, Y, and m are as defined herein.

In some embodiments, pharmaceutical compositions are provided which comprise a compound described herein (e.g., a compound of Formula (I)), or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient.

In certain embodiments, compounds described herein inhibit activity of an arginine methyltransferase (RMT) (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8). In certain embodiments, methods of inhibiting an arginine methyltransferase are provided which comprise contacting the arginine methyltransferase with an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof. The RMT may be purified or crude, and may be present in a cell, tissue, or a subject. Thus, such methods encompass inhibition of RMT activity both in vitro and in vivo. In certain embodiments, the RMT is wild-type. In certain embodiments, the RMT is overexpressed. In certain embodiments, the RMT is a mutant. In certain embodiments, the RMT is in a cell. In certain embodiments, the RMT is in an animal, e.g., a human. In some embodiments, the RMT is expressed at normal levels in a subject, but the subject would benefit from RMT inhibition (e.g., because the subject has one or more mutations in an RMT substrate that causes an increase in methylation of the substrate with normal levels of RMT). In some embodiments, the RMT is in a subject known or identified as having abnormal RMT activity (e.g., overexpression).

In certain embodiments, methods of modulating gene expression in a cell are provided which comprise contacting a cell with an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof. In certain embodiments, the cell in culture in vitro. In certain embodiments, cell is in an animal, e.g., a human.

In certain embodiments, methods of modulating transcription in a cell are provided which comprise contacting a cell with an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof. In certain embodiments, the cell in culture in vitro. In certain embodiments, the cell is in an animal, e.g., a human.

In some embodiments, methods of treating an RMT-mediated disorder (e.g., a PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8-mediated disorder) are provided which comprise administering to a subject suffering from an RMT-mediated disorder an effective amount of a compound described herein (e.g., a compound of Formula (I)), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof. In certain embodiments, the RMT-mediated disorder is a proliferative disorder. In certain embodiments, compounds described herein are useful for treating cancer. In certain embodiments, compounds described herein are useful for treating breast cancer, prostate cancer, lung cancer, colon cancer, bladder cancer, or leukemia. In certain embodiments, the RMT-mediated disorder is a muscular disorder. In certain embodiments, the RMT-mediated disorder is an autoimmune disorder. In certain embodiments, the RMT-mediated disorder is a neurological disorder. In certain embodiments, the RMT-mediated disorder is a vascular disorder. In certain embodiments, the RMT-mediated disorder is a metabolic disorder.

Compounds described herein are also useful for the study of arginine methyltransferases in biological and pathological phenomena, the study of intracellular signal transduction pathways mediated by arginine methyltransferases, and the comparative evaluation of new RMT inhibitors.

This application refers to various issued patent, published patent applications, journal articles, and other publications, all of which are incorporated herein by reference.

Definitions of specific functional groups and chemical terms are described in more detail below. The chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75^(th) Ed., inside cover, and specific functional groups are generally defined as described therein. Additionally, general principles of organic chemistry, as well as specific functional moieties and reactivity, are described in Thomas Sorrell, Organic Chemistry, University Science Books, Sausalito, 1999; Smith and March, March's Advanced Organic Chemistry, 5^(th) Edition, John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive Organic Transformations, VCH Publishers, Inc., New York, 1989; and Carruthers, Some Modern Methods of Organic Synthesis, 3^(rd) Edition, Cambridge University Press, Cambridge, 1987.

Compounds described herein can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e.g., enantiomers and/or diastereomers. For example, the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer. Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses. See, for example, Jacques et al., Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, Stereochemistry of Carbon Compounds (McGraw-Hill, NY, 1962); and Wilen, Tables of Resolving Agents and Optical Resolutions p. 268 (E. L. Eliel, Ed., Univ. of Notre Dame Press, Notre Dame, Ind. 1972). The present disclosure additionally encompasses compounds described herein as individual isomers substantially free of other isomers, and alternatively, as mixtures of various isomers.

It is to be understood that the compounds of the present invention may be depicted as different tautomers. It should also be understood that when compounds have tautomeric forms, all tautomeric forms are intended to be included in the scope of the present invention, and the naming of any compound described herein does not exclude any tautomer form.

Unless otherwise stated, structures depicted herein are also meant to include compounds that differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of hydrogen by deuterium or tritium, replacement of ¹⁹F with ¹⁸F, or the replacement of a carbon by a ¹³C- or ¹⁴C-enriched carbon are within the scope of the disclosure. Such compounds are useful, for example, as analytical tools or probes in biological assays.

“Radical” refers to a point of attachment on a particular group. Radical includes divalent radicals of a particular group.

When a range of values is listed, it is intended to encompass each value and sub-range within the range. For example “C₁₋₆ alkyl” is intended to encompass, C₁, C₂, C₃, C₄, C₅, C₆, C₁₋₆, C₁₋₅, C₁₋₄, C₁₋₃, C₁₋₂, C₂₋₆, C₂₋₅, C₂₋₄, C₂₋₃, C₃₋₆, C₃₋₅, C₃₋₄, C₄₋₆, C₄₋₅, and C₅₋₆ alkyl.

“Alkyl” refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 20 carbon atoms (“C₁₋₂₀ alkyl”). In some embodiments, an alkyl group has 1 to 10 carbon atoms (“C₁₋₁₀ alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms (“C₁₋₉ alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms (“C₁₋₈ alkyl”). In some embodiments, an alkyl group has 1 to 7 carbon atoms (“C₁₋₇ alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“C₁₋₆ alkyl”). In some embodiments, an alkyl group has 1 to 5 carbon atoms (“C₁₋₅ alkyl”). In some embodiments, an alkyl group has 1 to 4 carbon atoms (“C₁₋₄ alkyl”). In some embodiments, an alkyl group has 1 to 3 carbon atoms (“C₁₋₃ alkyl”). In some embodiments, an alkyl group has 1 to 2 carbon atoms (“C₁₋₂ alkyl”). In some embodiments, an alkyl group has 1 carbon atom (“C₁ alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C₂₋₆ alkyl”). Examples of C₁₋₆ alkyl groups include methyl (C₁), ethyl (C₂), n-propyl (C₃), isopropyl (C₃), n-butyl (C₄), tert-butyl (C₄), sec-butyl (C₄), iso-butyl (C₄), n-pentyl (C₅), 3-pentanyl (C₅), amyl (C₅), neopentyl (C₅), 3-methyl-2-butanyl (C₅), tertiary amyl (C₅), and n-hexyl (C₆). Additional examples of alkyl groups include n-heptyl (C₇), n-octyl (C₈) and the like. In certain embodiments, each instance of an alkyl group is independently optionally substituted, e.g., unsubstituted (an “unsubstituted alkyl”) or substituted (a “substituted alkyl”) with one or more substituents. In certain embodiments, the alkyl group is unsubstituted C₁₋₁₀ alkyl (e.g., —CH₃). In certain embodiments, the alkyl group is substituted C₁₋₁₀ alkyl.

In some embodiments, an alkyl group is substituted with one or more halogens. “Perhaloalkyl” is a substituted alkyl group as defined herein wherein all of the hydrogen atoms are independently replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo. In some embodiments, the alkyl moiety has 1 to 8 carbon atoms (“C₁₋₈ perhaloalkyl”). In some embodiments, the alkyl moiety has 1 to 6 carbon atoms (“C₁₋₆ perhaloalkyl”). In some embodiments, the alkyl moiety has 1 to 4 carbon atoms (“C₁₋₄ perhaloalkyl”). In some embodiments, the alkyl moiety has 1 to 3 carbon atoms (“C₁₋₃ perhaloalkyl”). In some embodiments, the alkyl moiety has 1 to 2 carbon atoms (“C₁₋₂ perhaloalkyl”). In some embodiments, all of the hydrogen atoms are replaced with fluoro. In some embodiments, all of the hydrogen atoms are replaced with chloro. Examples of perhaloalkyl groups include —CF₃, —CF₂CF₃, —CF₂CF₂CF₃, —CCl₃, —CFCl₂, —CF₂C₁, and the like.

As used herein, “alkenyl” refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 20 carbon atoms and one or more carbon-carbon double bonds (e.g., 1, 2, 3, or 4 double bonds), and optionally one or more triple bonds (e.g., 1, 2, 3, or 4 triple bonds) (“C₂₋₂₀ alkenyl”). In certain embodiments, alkenyl does not comprise triple bonds. In some embodiments, an alkenyl group has 2 to 10 carbon atoms (“C₂₋₁₀ alkenyl”). In some embodiments, an alkenyl group has 2 to 9 carbon atoms (“C₂₋₉ alkenyl”). In some embodiments, an alkenyl group has 2 to 8 carbon atoms (“C₂₋₈ alkenyl”). In some embodiments, an alkenyl group has 2 to 7 carbon atoms (“C₂₋₇ alkenyl”). In some embodiments, an alkenyl group has 2 to 6 carbon atoms (“C₂₋₆ alkenyl”). In some embodiments, an alkenyl group has 2 to 5 carbon atoms (“C₂₋₅ alkenyl”). In some embodiments, an alkenyl group has 2 to 4 carbon atoms (“C₂₋₄ alkenyl”). In some embodiments, an alkenyl group has 2 to 3 carbon atoms (“C₂₋₃ alkenyl”). In some embodiments, an alkenyl group has 2 carbon atoms (“C₂ alkenyl”). The one or more carbon-carbon double bonds can be internal (such as in 2-butenyl) or terminal (such as in 1-butenyl). Examples of C₂₋₄ alkenyl groups include ethenyl (C₂), 1-propenyl (C₃), 2-propenyl (C₃), 1-butenyl (C₄), 2-butenyl (C₄), butadienyl (C₄), and the like. Examples of C₂₋₆ alkenyl groups include the aforementioned C₂₋₄ alkenyl groups as well as pentenyl (C₅), pentadienyl (C₅), hexenyl (C₆), and the like. Additional examples of alkenyl include heptenyl (C₇), octenyl (C₈), octatrienyl (C₈), and the like. In certain embodiments, each instance of an alkenyl group is independently optionally substituted, e.g., unsubstituted (an “unsubstituted alkenyl”) or substituted (a “substituted alkenyl”) with one or more substituents. In certain embodiments, the alkenyl group is unsubstituted C₂₋₁₀ alkenyl. In certain embodiments, the alkenyl group is substituted C₂₋₁₀ alkenyl.

As used herein, “alkynyl” refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 20 carbon atoms and one or more carbon-carbon triple bonds (e.g., 1, 2, 3, or 4 triple bonds), and optionally one or more double bonds (e.g., 1, 2, 3, or 4 double bonds) (“C₂₋₂₀ alkynyl”). In certain embodiments, alkynyl does not comprise double bonds. In some embodiments, an alkynyl group has 2 to 10 carbon atoms (“C₂₋₁₀ alkynyl”). In some embodiments, an alkynyl group has 2 to 9 carbon atoms (“C₂₋₉ alkynyl”). In some embodiments, an alkynyl group has 2 to 8 carbon atoms (“C₂₋₈ alkynyl”). In some embodiments, an alkynyl group has 2 to 7 carbon atoms (“C₂₋₇ alkynyl”). In some embodiments, an alkynyl group has 2 to 6 carbon atoms (“C₂₋₆ alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms (“C₂₋₅ alkynyl”). In some embodiments, an alkynyl group has 2 to 4 carbon atoms (“C₂₋₄ alkynyl”). In some embodiments, an alkynyl group has 2 to 3 carbon atoms (“C₂₋₃ alkynyl”). In some embodiments, an alkynyl group has 2 carbon atoms (“C₂ alkynyl”). The one or more carbon-carbon triple bonds can be internal (such as in 2-butynyl) or terminal (such as in 1-butynyl). Examples of C₂₋₄ alkynyl groups include, without limitation, ethynyl (C₂), 1-propynyl (C₃), 2-propynyl (C₃), 1-butynyl (C₄), 2-butynyl (C₄), and the like. Examples of C₂₋₄ alkenyl groups include the aforementioned C₂₋₄ alkynyl groups as well as pentynyl (C₅), hexynyl (C₆), and the like. Additional examples of alkynyl include heptynyl (C₇), octynyl (C₈), and the like. In certain embodiments, each instance of an alkynyl group is independently optionally substituted, e.g., unsubstituted (an “unsubstituted alkynyl”) or substituted (a “substituted alkynyl”) with one or more substituents. In certain embodiments, the alkynyl group is unsubstituted C₂₋₁₀ alkynyl. In certain embodiments, the alkynyl group is substituted C₂₋₁₀ alkynyl.

“Fused” or “ortho-fused” are used interchangeably herein, and refer to two rings that have two atoms and one bond in common, e.g.,

“Bridged” refers to a ring system containing (1) a bridgehead atom or group of atoms which connect two or more non-adjacent positions of the same ring; or (2) a bridgehead atom or group of atoms which connect two or more positions of different rings of a ring system and does not thereby form an ortho-fused ring, e.g.,

“Spiro” or “Spiro-fused” refers to a group of atoms which connect to the same atom of a carbocyclic or heterocyclic ring system (geminal attachment), thereby forming a ring, e.g.,

Spiro-fusion at a bridgehead atom is also contemplated.

“Carbocyclyl” or “carbocyclic” refers to a radical of a non-aromatic cyclic hydrocarbon group having from 3 to 14 ring carbon atoms (“C₃₋₁₄ carbocyclyl”) and zero heteroatoms in the non-aromatic ring system. In certain embodiments, a carbocyclyl group refers to a radical of a non-aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C₃₋₁₀ carbocyclyl”) and zero heteroatoms in the non-aromatic ring system. In some embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms (“C₃₋₈ carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms (“C₃₋₆ carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms (“C₃₋₆ carbocyclyl”). In some embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms (“C₅₋₁₀ carbocyclyl”). Exemplary C₃₋₆ carbocyclyl groups include, without limitation, cyclopropyl (C₃), cyclopropenyl (C₃), cyclobutyl (C₄), cyclobutenyl (C₄), cyclopentyl (C₅), cyclopentenyl (C₅), cyclohexyl (C₆), cyclohexenyl (C₆), cyclohexadienyl (C₆), and the like. Exemplary C₃₋₈ carbocyclyl groups include, without limitation, the aforementioned C₃₋₆ carbocyclyl groups as well as cycloheptyl (C₇), cycloheptenyl (C₇), cycloheptadienyl (C₇), cycloheptatrienyl (C₇), cyclooctyl (C₈), cyclooctenyl (C₈), bicyclo[2.2.1]heptanyl (C₇), bicyclo[2.2.2]octanyl (C₈), and the like. Exemplary C₃₋₁₀ carbocyclyl groups include, without limitation, the aforementioned C₃₋₈ carbocyclyl groups as well as cyclononyl (C₉), cyclononenyl (C₉), cyclodecyl (C₁₀), cyclodecenyl (C₁₀), octahydro-1H-indenyl (C₉), decahydronaphthalenyl (C₁₀), spiro[4.5]decanyl (C₁₀), and the like. As the foregoing examples illustrate, in certain embodiments, the carbocyclyl group is either monocyclic (“monocyclic carbocyclyl”) or contain a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) and can be saturated or can be partially unsaturated. “Carbocyclyl” also includes ring systems wherein the carbocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclyl ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring system. In certain embodiments, each instance of a carbocyclyl group is independently optionally substituted, e.g., unsubstituted (an “unsubstituted carbocyclyl”) or substituted (a “substituted carbocyclyl”) with one or more substituents. In certain embodiments, the carbocyclyl group is unsubstituted C₃₋₁₀ carbocyclyl. In certain embodiments, the carbocyclyl group is a substituted C₃₋₁₀ carbocyclyl.

In some embodiments, “carbocyclyl” is a monocyclic, saturated carbocyclyl group having from 3 to 14 ring carbon atoms (“C₃₋₁₄ cycloalkyl”). In some embodiments, “carbocyclyl” is a monocyclic, saturated carbocyclyl group having from 3 to 10 ring carbon atoms (“C₃₋₁₀ cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms (“C₃₋₈ cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms (“C₃₋₆ cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C₅₋₆ cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms (“C₅₋₁₀ cycloalkyl”). Examples of C₅₋₆ cycloalkyl groups include cyclopentyl (C₅) and cyclohexyl (C₅). Examples of C₃₋₆ cycloalkyl groups include the aforementioned C₅₋₆ cycloalkyl groups as well as cyclopropyl (C₃) and cyclobutyl (C₄). Examples of C₃₋₈ cycloalkyl groups include the aforementioned C₃₋₆ cycloalkyl groups as well as cycloheptyl (C₇) and cyclooctyl (C₈). In certain embodiments, each instance of a cycloalkyl group is independently unsubstituted (an “unsubstituted cycloalkyl”) or substituted (a “substituted cycloalkyl”) with one or more substituents. In certain embodiments, the cycloalkyl group is unsubstituted C₃₋₁₀ cycloalkyl. In certain embodiments, the cycloalkyl group is substituted C₃₋₁₀ cycloalkyl.

“Heterocyclyl” or “heterocyclic” refers to a radical of a 3- to 14-membered non-aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“3-14 membered heterocyclyl”). In certain embodiments, heterocyclyl or heterocyclic refers to a radical of a 3-10 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“3-10 membered heterocyclyl”). In heterocyclyl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. A heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic heterocyclyl”), and can be saturated or can be partially unsaturated. Heterocyclyl bicyclic ring systems can include one or more heteroatoms in one or both rings. “Heterocyclyl” also includes ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclyl ring, or ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclyl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclyl ring system. In certain embodiments, each instance of heterocyclyl is independently optionally substituted, e.g., unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a “substituted heterocyclyl”) with one or more substituents. In certain embodiments, the heterocyclyl group is unsubstituted 3-10 membered heterocyclyl. In certain embodiments, the heterocyclyl group is substituted 3-10 membered heterocyclyl.

In some embodiments, a heterocyclyl group is a 5-10 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-10 membered heterocyclyl”). In some embodiments, a heterocyclyl group is a 5-8 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-8 membered heterocyclyl”). In some embodiments, a heterocyclyl group is a 5-6 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heterocyclyl”). In some embodiments, the 5-6 membered heterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has one ring heteroatom selected from nitrogen, oxygen, and sulfur.

Exemplary 3-membered heterocyclyl groups containing one heteroatom include, without limitation, azirdinyl, oxiranyl, and thiiranyl. Exemplary 4-membered heterocyclyl groups containing one heteroatom include, without limitation, azetidinyl, oxetanyl, and thietanyl. Exemplary 5-membered heterocyclyl groups containing one heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl, and pyrrolyl-2,5-dione. Exemplary 5-membered heterocyclyl groups containing two heteroatoms include, without limitation, dioxolanyl, oxasulfuranyl, disulfuranyl, and oxazolidin-2-one. Exemplary 5-membered heterocyclyl groups containing three heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary 6-membered heterocyclyl groups containing one heteroatom include, without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl. Exemplary 6-membered heterocyclyl groups containing two heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, and dioxanyl. Exemplary 6-membered heterocyclyl groups containing three heteroatoms include, without limitation, triazinanyl. Exemplary 7-membered heterocyclyl groups containing one heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl. Exemplary 8-membered heterocyclyl groups containing one heteroatom include, without limitation, azocanyl, oxecanyl, and thiocanyl. Exemplary 5-membered heterocyclyl groups fused to a C₆ aryl ring (also referred to herein as a 5,6-bicyclic heterocyclic ring) include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, benzoxazolinonyl, and the like. Exemplary 6-membered heterocyclyl groups fused to an aryl ring (also referred to herein as a 6,6-bicyclic heterocyclic ring) include, without limitation, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and the like.

“Aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 it electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system (“C₆₋₁₄ aryl”). In some embodiments, an aryl group has six ring carbon atoms (“C₆ aryl”; e.g., phenyl). In some embodiments, an aryl group has ten ring carbon atoms (“C₁₀ aryl”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). In some embodiments, an aryl group has fourteen ring carbon atoms (“C₁₄ aryl”; e.g., anthracyl). “Aryl” also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system. In certain embodiments, each instance of an aryl group is independently optionally substituted, e.g., unsubstituted (an “unsubstituted aryl”) or substituted (a “substituted aryl”) with one or more substituents. In certain embodiments, the aryl group is unsubstituted C₆₋₁₄ aryl. In certain embodiments, the aryl group is substituted C₆₋₁₄ aryl.

“Heteroaryl” refers to a radical of a 5-14 membered monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6 or 10 it electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-14 membered heteroaryl”). In certain embodiments, heteroaryl refers to a radical of a 5-10 membered monocyclic or bicyclic 4n+2 aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur (“5-10 membered heteroaryl”). In heteroaryl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. Heteroaryl bicyclic ring systems can include one or more heteroatoms in one or both rings. “Heteroaryl” includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system. “Heteroaryl” also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused (aryl/heteroaryl) ring system. Bicyclic heteroaryl groups wherein one ring does not contain a heteroatom (e.g., indolyl, quinolinyl, carbazolyl, and the like) the point of attachment can be on either ring, e.g., either the ring bearing a heteroatom (e.g., 2-indolyl) or the ring that does not contain a heteroatom (e.g., 5-indolyl).

In some embodiments, a heteroaryl group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”). In some embodiments, a heteroaryl group is a 5-8 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-8 membered heteroaryl”). In some embodiments, a heteroaryl group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”). In some embodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur. In certain embodiments, each instance of a heteroaryl group is independently optionally substituted, e.g., unsubstituted (“unsubstituted heteroaryl”) or substituted (“substituted heteroaryl”) with one or more substituents. In certain embodiments, the heteroaryl group is unsubstituted 5-14 membered heteroaryl. In certain embodiments, the heteroaryl group is substituted 5-14 membered heteroaryl.

Exemplary 5-membered heteroaryl groups containing one heteroatom include, without limitation, pyrrolyl, furanyl and thiophenyl. Exemplary 5-membered heteroaryl groups containing two heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl. Exemplary 5-membered heteroaryl groups containing three heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary 5-membered heteroaryl groups containing four heteroatoms include, without limitation, tetrazolyl. Exemplary 6-membered heteroaryl groups containing one heteroatom include, without limitation, pyridinyl. Exemplary 6-membered heteroaryl groups containing two heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl. Exemplary 6-membered heteroaryl groups containing three or four heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively. Exemplary 7-membered heteroaryl groups containing one heteroatom include, without limitation, azepinyl, oxepinyl, and thiepinyl. Exemplary 6,6-bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl. Exemplary 5,6-bicyclic heteroaryl groups include, without limitation, any one of the following formulae:

In any of the monocyclic or bicyclic heteroaryl groups, the point of attachment can be any carbon or nitrogen atom, as valency permits.

“Partially unsaturated” refers to a group that includes at least one double or triple bond. The term “partially unsaturated” is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aromatic groups (e.g., aryl or heteroaryl groups) as herein defined. Likewise, “saturated” refers to a group that does not contain a double or triple bond, i.e., contains all single bonds.

In some embodiments, alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, as defined herein, are optionally substituted (e.g., “substituted” or “unsubstituted” alkyl, “substituted” or “unsubstituted” alkenyl, “substituted” or “unsubstituted” alkynyl, “substituted” or “unsubstituted” carbocyclyl, “substituted” or “unsubstituted” heterocyclyl, “substituted” or “unsubstituted” aryl or “substituted” or “unsubstituted” heteroaryl group). In general, the term “substituted”, whether preceded by the term “optionally” or not, means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction. Unless otherwise indicated, a “substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position. The term “substituted” is contemplated to include substitution with all permissible substituents of organic compounds, including any of the substituents described herein that results in the formation of a stable compound. The present disclosure contemplates any and all such combinations in order to arrive at a stable compound. For purposes of this disclosure, heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety.

Exemplary carbon atom substituents include, but are not limited to, halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(aa), —ON(R^(bb))₂, —N(R^(bb))₂, —N(R^(bb))₃ ⁺X⁻, —N(OR^(cc))R^(bb), —SH, —SR^(aa), —SSR^(cc), —C(═O)R^(aa), —CO₂H, —CHO, —C(OR^(cc))₂, —CO₂R^(aa), —OC(═O)R^(aa), —OCO₂R^(aa), —C(═O)N(R^(bb))₂, —OC(═O)N(R^(bb))₂, —NR^(bb)C(═O)R^(aa), —NR^(bb)CO₂R^(aa), —NR^(bb)C(═O)N(R^(bb))₂, —C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —OC(═NR^(bb))R^(aa), —OC(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —OC(═NR^(bb))N(R^(bb))₂, —NR^(bb)C(═NR^(bb))N(R^(bb))₂, —C(═O)NR^(bb)SO₂R^(aa), —NR^(bb)SO₂R^(aa), —SO₂N(R^(bb))₂, —SO₂R^(aa), —SO₂OR^(aa), —OSO₂R^(aa), —S(═O)R^(aa), —OS(═O)R^(aa), —Si(R^(aa))₃, —OSi(R^(aa))₃—C(═S)N(R^(bb))₂, —C(═O)SR^(aa), —C(═S)SR^(aa), —SC(═S)SR^(aa), —SC(═O)SR^(aa), —OC(═O)SR^(aa), —SC(═O)OR^(aa), —SC(═O)R^(aa), —P(═O)₂R^(aa), —OP(═O)₂R^(aa), —P(═O)(R^(aa))₂, —OP(═O)(R^(aa))₂, —OP(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂, —OP(═O)₂N(R^(bb))₂, —P(═O)(NR^(bb))₂, —OP(═O)(NR^(bb))₂, —NR^(bb)P(═O)(OR^(cc))₂, —NR^(bb)P(═O)(NR^(bb))₂, —P(R^(cc))₂, —P(R^(cc))₃, —OP(R^(cc))₂, —OP(R^(cc))₃, —B(R^(aa))₂, —B(OR^(cc))₂, —BR^(aa)(OR^(cc)), C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

or two geminal hydrogens on a carbon atom are replaced with the group ═O, ═S, ═NN(R^(bb))₂, ═NNR^(bb)C(═O)R^(aa), ═NNR^(bb)C(═O)OR^(aa), ═NNR^(bb)S(═O)₂R^(aa), ═NR^(bb), or ═NOR^(cc);

each instance of R^(aa) is, independently, selected from C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, or two R^(aa) groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(bb) is, independently, selected from hydrogen, —OH, —OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa), —SO₂R^(aa), —C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc), —SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), C(═S)SR^(cc), —P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)₂N(R^(cc))₂, —P(═O)(NR^(cc))₂, C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, or two R^(bb) groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(cc) is, independently, selected from hydrogen, C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, or two R^(cc) groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(dd) is, independently, selected from halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(ee), —ON(R^(ff))₂, —N(R^(ff))₂, —N(R^(ff))₃ ⁺X⁻, —N(OR^(ee))R^(ff), —SH, —SR^(ee), —SSR^(ee), —C(═O)R^(ee), —CO₂H, —CO₂R^(ee), —OC(═O)R^(ee), —OCO₂R^(ee), —C(═O)N(R^(ff))₂, —OC(═O)N(R^(ff))₂, —NR^(ff)C(═O)R^(ee), —NR^(ff)CO₂R^(ee), —NR^(ff)C(═O)N(R^(ff))₂, —C(═NR^(ff))OR^(ee), OC(═NR^(ff))R^(ee), —OC(═NR^(ff))OR^(ee), —C(═NR^(ff))N(R^(ff))₂, —OC(═NR^(ff))N(R^(ff))₂, —NR^(ff)C(═NR^(ff))N(R^(ff))₂, —NR^(ff)SO₂R^(ee), —SO₂N(R^(ff))₂, —SO₂R^(ee), —SO₂OR^(ee), —OSO₂R^(ee), —S(═O)R^(ee), —Si(R^(ee))₃, —OSi(R^(ee))₃, —C(═S)N(R^(ff))₂, —C(═O)SR^(ee), —C(═S)SR^(ee), —SC(═S)SR^(ee), —P(═O)₂R^(ee), —P(═O)(R^(ee))₂, —OP(═O)(R^(ee))₂, —OP(═O)(OR^(ee))₂, C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, 3-10 membered heterocyclyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg) groups, or two geminal R^(dd) substituents can be joined to form ═O or ═S;

each instance of R^(ee) is, independently, selected from C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, C₆₋₁₀ aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg) groups;

each instance of R^(ff) is, independently, selected from hydrogen, C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, 3-10 membered heterocyclyl, C₆ to aryl and 5-10 membered heteroaryl, or two R^(ff) groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg) groups; and

each instance of R^(gg) is, independently, halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OC₁₋₆ alkyl, —ON(C₁₋₆ alkyl)₂, —N(C₁₋₆ alkyl)₂, —N(C₁₋₆ alkyl)₃+X⁻, —NH(C₁₋₆ alkyl)₂+X⁻, —NH₂(C₁₋₆ alkyl)⁺X⁻, —NH₃+X⁻, —N(OC₁₋₆ alkyl)(C₁₋₆ alkyl), —N(OH)(C₁₋₆ alkyl), —NH(OH), —SH, —SC₁₋₆ alkyl, —SS(C₁₋₆ alkyl), —C(═O)(C₁₋₆ alkyl), —CO₂H, —CO₂(C₁₋₆ alkyl), —OC(═O)(C₁₋₆ alkyl), —OCO₂(C₁₋₆ alkyl), —C(═O)NH₂, —C(═O)N(C₁₋₆ alkyl)₂, —OC(═O)NH(C₁₋₆ alkyl), —NHC(═O)(C₁₋₆ alkyl), —N(C₁₋₆ alkyl)C(═O)(C₁₋₆ alkyl), —NHCO₂(C₁₋₆ alkyl), —NHC(═O)N(C₁₋₆ alkyl)₂, —NHC(═O)NH(C₁₋₆ alkyl), —NHC(═O)NH₂, —C(═NH)O(C₁₋₆ alkyl), —OC(═NH)(C₁₋₆ alkyl), —OC(═NH)OC₁₋₆ alkyl, —C(═NH)N(C₁₋₆ alkyl)₂, —C(═NH)NH(C₁₋₆ alkyl), —C(═NH)NH₂, —OC(═NH)N(C₁₋₆ alkyl)₂, —OC(NH)NH(C₁₋₆ alkyl), —OC(NH)NH₂, —NHC(NH)N(C₁₋₆ alkyl)₂, —NHC(═NH)NH₂, —NHSO₂(C₁₋₆ alkyl), —SO₂N(C₁₋₆ alkyl)₂, —SO₂NH(C₁₋₆ alkyl), —SO₂NH₂, —SO₂C₁₋₆ alkyl, —SO₂OC₁₋₆ alkyl, —OSO₂C₁₋₆ alkyl, —SOC₁₋₆ alkyl, —Si(C₁₋₄ alkyl)₃, —OSi(C₁₋₆ alkyl)₃—C(═S)N(C₁₋₆ alkyl)₂, C(═S)NH(C₁₋₆ alkyl), C(═S)NH₂, —C(═O)S(C₁₋₆ alkyl), —C(═S)SC₁₋₆ alkyl, —SC(═S)SC₁₋₆ alkyl, —P(═O)₂(C₁₋₆ alkyl), —P(═O)(C₁₋₆ alkyl)₂, —OP(═O)(C₁₋₆ alkyl)₂, —OP(═O)(OC₁₋₆ alkyl)₂, C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, C₆₋₁₀ aryl, 3-10 membered heterocyclyl, 5-10 membered heteroaryl; or two geminal R^(gg) substituents can be joined to form ═O or ═S; wherein X is a counterion.

A “counterion” or “anionic counterion” is a negatively charged group associated with a cationic quaternary amino group in order to maintain electronic neutrality. Exemplary counterions include halide ions (e.g., F⁻, Cl⁻, Br⁻, I⁻), NO₃ ⁻, ClO₄ ⁻, OH⁻, H₂PO₄ ⁻, HSO₄ ⁻, sulfonate ions (e.g., methansulfonate, trifluoromethanesulfonate, p-toluenesulfonate, benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate, naphthalene-1-sulfonic acid-5-sulfonate, ethan-1-sulfonic acid-2-sulfonate, and the like), and carboxylate ions (e.g., acetate, ethanoate, propanoate, benzoate, glycerate, lactate, tartrate, glycolate, and the like).

“Halo” or “halogen” refers to fluorine (fluoro, —F), chlorine (chloro, —Cl), bromine (bromo, —Br), or iodine (iodo, —I).

Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quarternary nitrogen atoms. Exemplary nitrogen atom substitutents include, but are not limited to, hydrogen, —OH, —OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa), —SO₂R^(aa), —C(═NR^(bb))R^(aa), —C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc), —SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), C(═S)SR^(cc), —P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)₂N(R^(cc))₂, —P(═O)(NR^(cc))₂, C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, or two R^(cc) groups attached to a nitrogen atom are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups, and wherein R^(aa), R^(bb), R^(cc) and R^(dd) are as defined above.

In certain embodiments, the substituent present on a nitrogen atom is a nitrogen protecting group (also referred to as an amino protecting group). Nitrogen protecting groups include, but are not limited to, —OH, —OR^(aa), —N(R^(cc))₂, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa), —SO₂R^(aa), —C(═NR^(cc))R^(aa), —C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc), SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc), C₁₋₁₀ alkyl (e.g., aralkyl, heteroaralkyl), C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆14 aryl, and 5-14 membered heteroaryl groups, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aralkyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups, and wherein R^(aa), R^(bb), R^(cc), and R^(dd) are as defined herein. Nitrogen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3^(rd) edition, John Wiley & Sons, 1999, incorporated herein by reference.

Amide nitrogen protecting groups (e.g., —C(═O)R^(aa)) include, but are not limited to, formamide, acetamide, chloroacetamide, trichloroacetamide, trifluoroacetamide, phenylacetamide, 3-phenylpropanamide, picolinamide, 3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide, p-phenylbenzamide, o-nitophenylacetamide, o-nitrophenoxyacetamide, acetoacetamide, (N′-dithiobenzyloxyacylamino)acetamide, 3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide, 2-methyl-2-(o-nitrophenoxy)propanamide, 2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide, 3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethionine, o-nitrobenzamide, and o-(benzoyloxymethyl)benzamide.

Carbamate nitrogen protecting groups (e.g., —C(═O)OR^(aa)) include, but are not limited to, methyl carbamate, ethyl carbamante, 9-fluorenylmethyl carbamate (Fmoc), 9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluoroenylmethyl carbamate, 2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methyl carbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc), 2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ), 1-(1-adamantyl)-1-methylethyl carbamate (Adpoc), 1,1-dimethyl-2-haloethyl carbamate, 1,1-dimethyl-2,2-dibromoethyl carbamate (DB-t-BOC), 1,1-dimethyl-2,2,2-trichloroethyl carbamate (TCBOC), 1-methyl-1-(4-biphenylyl)ethyl carbamate (Bpoc), 1-(3,5-di-t-butylphenyl)-1-methylethyl carbamate (t-Bumeoc), 2-(2′- and 4′-pyridyl)ethyl carbamate (Pyoc), 2-(N,N-dicyclohexylcarboxamido)ethyl carbamate, t-butyl carbamate (BOC), 1-adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl carbamate (Alloc), 1-isopropylallyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate (Noc), 8-quinolyl carbamate, N-hydroxypiperidinyl carbamate, alkyldithio carbamate, benzyl carbamate (Cbz), p-methoxybenzyl carbamate (Moz), p-nitobenzyl carbamate, p-bromobenzyl carbamate, p-chlorobenzyl carbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfinylbenzyl carbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate, 2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate, 2-(p-toluenesulfonyl)ethyl carbamate, [2-(1,3-dithianyl)]methyl carbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc), 2,4-dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate (Peoc), 2-triphenylphosphonioisopropyl carbamate (Ppoc), 1,1-dimethyl-2-cyanoethyl carbamate, m-chloro-p-acyloxybenzyl carbamate, p-(dihydroxyboryl)benzyl carbamate, 5-benzisoxazolylmethyl carbamate, 2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), m-nitrophenyl carbamate, 3,5-dimethoxybenzyl carbamate, o-nitrobenzyl carbamate, 3,4-dimethoxy-6-nitrobenzyl carbamate, phenyl(o-nitrophenyl)methyl carbamate, t-amyl carbamate, S-benzyl thiocarbamate, p-cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl carbamate, p-decyloxybenzyl carbamate, 2,2-dimethoxyacylvinyl carbamate, o-(N,N-dimethylcarboxamido)benzyl carbamate, 1,1-dimethyl-3-(N,N-dimethylcarboxamido)propyl carbamate, 1,1-dimethylpropynyl carbamate, di(2-pyridyl)methyl carbamate, 2-furanylmethyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p-(p′-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate, 1-methylcyclohexyl carbamate, 1-methyl-1-cyclopropylmethyl carbamate, 1-methyl-1-(3,5-dimethoxyphenyl)ethyl carbamate, 1-methyl-1-(p-phenylazophenyl)ethyl carbamate, 1-methyl-1-phenylethyl carbamate, 1-methyl-1-(4-pyridyl)ethyl carbamate, phenyl carbamate, p-(phenylazo)benzyl carbamate, 2,4,6-tri-t-butylphenyl carbamate, 4-(trimethylammonium)benzyl carbamate, and 2,4,6-trimethylbenzyl carbamate.

Sulfonamide nitrogen protecting groups (e.g., —S(═O)₂R^(aa)) include, but are not limited to, p-toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6,-trimethyl-4-methoxybenzenesulfonamide (Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb), 2,6-dimethyl-4-methoxybenzenesulfonamide (Pme), 2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte), 4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide (Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds), 2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide (Ms), β-trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide, 4-(4′,8′-dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS), benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide.

Other nitrogen protecting groups include, but are not limited to, phenothiazinyl-(10)-acyl derivative, N′-p-toluenesulfonylaminoacyl derivative, N′-phenylaminothioacyl derivative, N-benzoylphenylalanyl derivative, N-acetylmethionine derivative, 4,5-diphenyl-3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, N-2,5-dimethylpyrrole, N-1,1,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5-substituted 1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted 1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substituted 3,5-dinitro-4-pyridone, N-methylamine, N-allylamine, N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), N-3-acetoxypropylamine, N-(1-isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammonium salts, N-benzylamine, N-di(4-methoxyphenyl)methylamine, N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr), N-[(4-methoxyphenyl)diphenylmethyl]amine (MMTr), N-9-phenylfluorenylamine (PhF), N-2,7-dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm), N-2-picolylamino N′-oxide, N-1,1-dimethylthiomethyleneamine, N-benzylideneamine, N-p-methoxybenzylideneamine, N-diphenylmethyleneamine, N-[(2-pyridyl)mesityl]methyleneamine, N—(N′,N′-dimethylaminomethylene)amine, N,N′-isopropylidenediamine, N-p-nitrobenzylideneamine, N-salicylideneamine, N-5-chlorosalicylideneamine, N-(5-chloro-2-hydroxyphenyl)phenylmethyleneamine, N-cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-1-cyclohexenyl)amine, N-borane derivative, N-diphenylborinic acid derivative, N-[phenyl(pentaacylchromium- or tungsten)acyl]amine, N-copper chelate, N-zinc chelate, N-nitroamine, N-nitrosoamine, amine N-oxide, diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt), diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzyl phosphoramidate, diphenyl phosphoramidate, benzenesulfenamide, o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide, triphenylmethylsulfenamide, and 3-nitropyridinesulfenamide (Npys).

In certain embodiments, the substituent present on an oxygen atom is an oxygen protecting group (also referred to as a hydroxyl protecting group). Oxygen protecting groups include, but are not limited to, —R^(aa), —N(R^(bb))₂, —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa), —C(═O)N(R^(bb))₂, —C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —S(═O)R^(aa), —SO₂R^(aa), Si(R^(aa))₃, —P(R^(cc))₂, —P(R^(cc))₃, —P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂, and —P(═O)(NR^(bb))₂, wherein R^(aa), R^(bb), and R^(cc) are as defined herein. Oxygen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by reference.

Exemplary oxygen protecting groups include, but are not limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t-butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM), p-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl, bis(2-chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3-bromotetrahydropyranyl, tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4-methoxytetrahydropyranyl (MTHP), 4-methoxytetrahydrothiopyranyl, 4-methoxytetrahydrothiopyranyl S,S-dioxide, 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl (CTMP), 1,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl, 2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl, 1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 1-methyl-1-methoxyethyl, 1-methyl-1-benzyloxyethyl, 1-methyl-1-benzyloxy-2-fluoroethyl, 2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2-(phenylselenyl)ethyl, t-butyl, allyl, p-chlorophenyl, p-methoxyphenyl, 2,4-dinitrophenyl, benzyl (Bn), p-methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl, p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl, p-phenylbenzyl, 2-picolyl, 4-picolyl, 3-methyl-2-picolyl N-oxido, diphenylmethyl, p,p′-dinitrobenzhydryl, 5-dibenzosuberyl, triphenylmethyl, α-naphthyldiphenylmethyl, p-methoxyphenyldiphenylmethyl, di(p-methoxyphenyl)phenylmethyl, tri(p-methoxyphenyl)methyl, 4-(4′-bromophenacyloxyphenyl)diphenylmethyl, 4,4′,4″-tris(4,5-dichlorophthalimidophenyl)methyl, 4,4′,4″-tris(levulinoyloxyphenyl)methyl, 4,4′,4″-tris(benzoyloxyphenyl)methyl, 3-(imidazol-1-yl)bis(4′,4″-dimethoxyphenyl)methyl, 1,1-bis(4-methoxyphenyl)-1′-pyrenylmethyl, 9-anthryl, 9-(9-phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryl, 1,3-benzodithiolan-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl (TIPS), dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS), dimethylthexylsilyl, t-butyldimethylsilyl (TBDMS), t-butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri-p-xylylsilyl, triphenylsilyl, diphenylmethylsilyl (DPMS), t-butylmethoxyphenylsilyl (TBMPS), formate, benzoylformate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate, 3-phenylpropionate, 4-oxopentanoate (levulinate), 4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4-methoxycrotonate, benzoate, p-phenylbenzoate, 2,4,6-trimethylbenzoate (mesitoate), methyl carbonate, 9-fluorenylmethyl carbonate (Fmoc), ethyl carbonate, 2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate (TMSEC), 2-(phenylsulfonyl)ethyl carbonate (Psec), 2-(triphenylphosphonio)ethyl carbonate (Peoc), isobutyl carbonate, vinyl carbonate, allyl carbonate, t-butyl carbonate (BOC), p-nitrophenyl carbonate, benzyl carbonate, p-methoxybenzyl carbonate, 3,4-dimethoxybenzyl carbonate, o-nitrobenzyl carbonate, p-nitrobenzyl carbonate, S-benzyl thiocarbonate, 4-ethoxy-1-napththyl carbonate, methyl dithiocarbonate, 2-iodobenzoate, 4-azidobutyrate, 4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate, 2-formylbenzenesulfonate, 2-(methylthiomethoxy)ethyl, 4-(methylthiomethoxy)butyrate, 2-(methylthiomethoxymethyl)benzoate, 2,6-dichloro-4-methylphenoxyacetate, 2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate, 2,4-bis(1,1-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, isobutyrate, monosuccinoate, (E)-2-methyl-2-butenoate, o-(methoxyacyl)benzoate, α-naphthoate, nitrate, alkyl N,N,N′,N′-tetramethylphosphorodiamidate, alkyl N-phenylcarbamate, borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts).

In certain embodiments, the substituent present on a sulfur atom is a sulfur protecting group (also referred to as a thiol protecting group). Sulfur protecting groups include, but are not limited to, —R^(aa), —N(R^(bb))₂, —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa), —C(═O)N(R^(bb))₂, —C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —S(═O)R^(aa), —SO₂R^(aa), Si(R^(aa))₃, —P(R^(cc))₂, —P(R^(cc))₃, —P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂, and —P(═O)(NR^(bb))₂, wherein R^(aa), R^(bb), and R^(cc) are as defined herein. Sulfur protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3^(rd) edition, John Wiley & Sons, 1999, incorporated herein by reference.

These and other exemplary substituents are described in more detail in the Detailed Description, Examples, and claims. The present disclosure is not intended to be limited in any manner by the above exemplary listing of substituents.

“Pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and other animals without undue toxicity, irritation, allergic response, and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, Berge et al. describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences (1977) 66:1-19. Pharmaceutically acceptable salts of the compounds describe herein include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N⁺(C₁₋₄alkyl)₄ salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, quaternary salts.

A “subject” to which administration is contemplated includes, but is not limited to, humans (e.g., a male or female of any age group, e.g., a pediatric subject (e.g, infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult or senior adult)) and/or other non-human animals, for example, non-human mammals (e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs), birds (e.g., commercially relevant birds such as chickens, ducks, geese, and/or turkeys), rodents (e.g., rats and/or mice), reptiles, amphibians, and fish. In certain embodiments, the non-human animal is a mammal. The non-human animal may be a male or female at any stage of development. A non-human animal may be a transgenic animal.

“Condition,” “disease,” and “disorder” are used interchangeably herein.

“Treat,” “treating” and “treatment” encompasses an action that occurs while a subject is suffering from a condition which reduces the severity of the condition or retards or slows the progression of the condition (“therapeutic treatment”). “Treat,” “treating” and “treatment” also encompasses an action that occurs before a subject begins to suffer from the condition and which inhibits or reduces the severity of the condition (“prophylactic treatment”).

An “effective amount” of a compound refers to an amount sufficient to elicit the desired biological response, e.g., treat the condition. As will be appreciated by those of ordinary skill in this art, the effective amount of a compound described herein may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the condition being treated, the mode of administration, and the age and health of the subject. An effective amount encompasses therapeutic and prophylactic treatment.

A “therapeutically effective amount” of a compound is an amount sufficient to provide a therapeutic benefit in the treatment of a condition or to delay or minimize one or more symptoms associated with the condition. A therapeutically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other therapies, which provides a therapeutic benefit in the treatment of the condition. The term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of the condition, or enhances the therapeutic efficacy of another therapeutic agent.

A “prophylactically effective amount” of a compound is an amount sufficient to prevent a condition, or one or more symptoms associated with the condition or prevent its recurrence. A prophylactically effective amount of a compound means an amount of a therapeutic agent, alone or in combination with other agents, which provides a prophylactic benefit in the prevention of the condition. The term “prophylactically effective amount” can encompass an amount that improves overall prophylaxis or enhances the prophylactic efficacy of another prophylactic agent.

As used herein, the term “methyltransferase” represents transferase class enzymes that are able to transfer a methyl group from a donor molecule to an acceptor molecule, e.g., an amino acid residue of a protein or a nucleic base of a DNA molecule. Methytransferases typically use a reactive methyl group bound to sulfur in S-adenosyl methionine (SAM) as the methyl donor. In some embodiments, a methyltransferase described herein is a protein methyltransferase. In some embodiments, a methyltransferase described herein is a histone methyltransferase. Histone methyltransferases (HMT) are histone-modifying enzymes, (including histone-lysine N-methyltransferase and histone-arginine N-methyltransferase), that catalyze the transfer of one or more methyl groups to lysine and arginine residues of histone proteins. In certain embodiments, a methyltransferase described herein is a histone-arginine N-methyltransferase.

As generally described above, provided herein are compounds useful as arginine methyltransferase (RMT) inhibitors. In some embodiments, the present disclosure provides a compound of Formula (I):

wherein:

X is N—R₂ and Y is N; or

X is N and Y is N—R₂;

each instance of R₁ is independently selected from the group consisting of hydrogen, halogen, —N₃, —CN, —NO₂, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, —OR^(A), —N(R^(B))₂, —SR^(A), —C(═O)R^(A), —C(═O)OR^(A), —C(═O)SR^(A), —C(═O)N(R^(B))₂, —C(═O)N(R^(B))N(R^(B))₂, —OC(═O)R^(A), —OC(═O)N(R^(B))₂, —NR^(B)C(═O)R^(A), —NR^(B)C(═O)N(R^(B))₂, —NR^(B)C(═O)N(R^(B))N(R^(B))₂, —NR^(B)C(═O)OR^(A), —SC(═O)R^(A), —C(═NR^(B))R^(A), —C(═NNR^(B))R^(A), —C(═NOR^(A))R^(A), —C(═NR^(B))N(R^(B))₂, —NR^(B)C(═NR^(B))R^(B), —C(═S)R^(A), —C(═S)N(R^(B))₂, —NR^(B)C(═S)R^(A), —S(═O)R^(A), —OS(═O)₂R^(A), —SO₂R^(A), —NR^(B)SO₂R^(A), —SO₂N(R^(B))₂, or —Z—R₄;

Z is a bond, —O—, —S—, —NR^(B)—, —NR^(B)C(═O)—, —C(═O)NR^(B)—, —OC(═O)NR^(B)—, NR^(B)C(═O)O—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, trans-CR^(C)═CR^(C)—, cis-CR^(C)═CR^(C)—, —C≡C—, —OC(R^(cc))₂—, —C(R^(cc))₂O—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(B)—, NR^(B)S(═O)₂—, or an optionally substituted C₁₋₈ hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NR^(B)—, —NR^(B)C(═O)—, —C(═O)NR^(B)—, —OC(═O)NR^(B)—, —NR^(B)C(═O)O—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(B)C(═S)—, —C(═S)NR^(B)—, trans-CR^(C)═CR^(C)—, cis-CR^(C)═CR^(C)—, —C≡C—, —OC(R^(C))₂—, —C(R^(C))₂O—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(B)—, —NR^(B)S(═O)₂—, wherein each instance of R^(C) is independently selected from the group consisting of hydrogen, halogen optionally substituted alkyl, optionally substituted alkenyl, optionally substituted carbocyclyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted heterocyclyl, and optionally substituted heteroaryl, or two R^(C) groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring;

R₄ is hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, —OR^(A), —N(R^(B))₂, —SR^(A), or an oxygen protecting group;

m is 0, 1, 2, 3, or 4;

R₂ is hydrogen, optionally substituted C₁₋₆ alkyl, optionally substituted C₂₋₆ alkenyl, optionally substituted C₂₋₆ alkynyl, optionally substituted C₃₋₇ cycloalkyl, optionally substituted 4- to 7-membered heterocyclyl; or optionally substituted C₁₋₄ alkyl-Cy;

R₃ is independently hydrogen, C₁₋₄ alkyl, or C₃₋₄ carbocylyl;

R_(x) is independently optionally substituted C₁₋₄ alkyl or optionally substituted C₃₋₄ carbocylyl;

-   -   each instance of R^(A) is independently selected from the group         consisting of hydrogen, optionally substituted acyl, optionally         substituted alkyl, optionally substituted alkenyl, optionally         substituted alkynyl, optionally substituted carbocyclyl,         optionally substituted aryl, optionally substituted         heterocyclyl, optionally substituted heteroaryl, optionally         substituted alkyl-Cy, an oxygen protecting group when attached         to an oxygen atom, and a sulfur protecting group when attached         to a sulfur atom;

each instance of R^(B) is independently selected from the group consisting of hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, and a nitrogen protecting group, or two R^(B) groups are taken together with their intervening atoms to form an optionally substituted heterocyclic ring; and

each instance of Cy is independently optionally substituted C₃₋₇ cycloalkyl, optionally substituted 4- to 7-membered heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl.

In certain embodiments, a provided compound is of Formula (II):

or a pharmaceutically acceptable salt thereof, wherein X, Y, Z, R₃, R_(x), and R₄ are as described herein.

In certain embodiments, a provided compound is of Formula (II-a):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x) and R₄ are as described herein.

In certain embodiments, a provided compound is of Formula (II-a1):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₄, and n are as described herein.

In certain embodiments, a provided compound is of Formula (II-a1-i):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, V₁, V₂, V₃, V₄, V₅, p, and n are as described herein.

In certain embodiments, a provided compound is of Formula (II-a1-ii):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, p, and n are as described herein.

In certain embodiments, a provided compound is of Formula (II-a1-iii)

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, p, and n are as described herein.

In certain embodiments, a provided compound is of Formula (II-a1-iv):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, p, and n are as described herein.

In certain embodiments, a provided compound is of Formula (II-a1-v):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, p, and n are as described herein.

In certain embodiments, a provided compound is of Formula (II-a2):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, R^(B), q, and n are as described herein.

In certain embodiments, a provided compound is of Formula (II-a3):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R^(A), and n are as described herein.

In certain embodiments, a provided compound is of Formula (II-a4):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, V₁-V₅, and p are as described herein.

In certain embodiments, a provided compound is of Formula (II-a4-i):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, and p are as described herein.

In certain embodiments, a provided compound is of Formula (II-a5):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₇, and A₁-A₅ are as described herein.

In certain embodiments, a provided compound is of Formula (II-a6):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₇, and A₁-A₄ are as described herein.

In certain embodiments, a provided compound is of Formula (II-b):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₄, and s are as described herein.

In certain embodiments, a provided compound is of Formula (II-b1):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), and R₄ are as described herein.

In certain embodiments, a provided compound is of Formula (II-b2):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), V₁, V₂, V₃, V₄, V₅, R₆, p, and s are as described herein.

In certain embodiments, a provided compound is of Formula (II-b2-i):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, p, and s are as described herein.

In certain embodiments, a provided compound is of Formula (II-b3):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, p, and s are as described herein.

In certain embodiments, a provided compound is of Formula (II-c):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₄, t, and R^(B) are as described herein.

In certain embodiments, a provided compound is of Formula (II-c1):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₄, and R^(B) are as described herein.

In certain embodiments, a provided compound is of Formula (II-c2):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, V₁, V₂, V₃, V₄, V₅, R^(B), p, and t are as described herein.

In certain embodiments, a provided compound is of Formula (II-c2-i):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, R^(B), p, and t are as described herein.

In certain embodiments, a provided compound is of Formula (II-c3):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₆, R^(B), q, and t are as described herein.

In certain embodiments, a provided compound is of Formula (II-d):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), and R₄ are as described herein.

In certain embodiments, a provided compound is of Formula (II-d1):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₇, and A₁-A₅ are as described herein.

In certain embodiments, a provided compound is of Formula (II-d2):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₇, and A₁-A₄ are as described herein.

In certain embodiments, a provided compound is of Formula (II-d3):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), R₇, and A₁-A₄ are as described herein.

In certain embodiments, a provided compound is of Formula (II-d4):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), and R₄ are as described herein.

In certain embodiments, a provided compound is of Formula (II-d5):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), and R₄ are as described herein, and i is 0, 1, 2, 3, 4, 5, 6, 7, or 8.

In certain embodiments, a provided compound is of Formula (II-d6):

or a pharmaceutically acceptable salt thereof, wherein X, Y, R₃, R_(x), and R₄ are as described herein, and i is 0, 1, 2, 3, 4, 5, 6, 7, or 8.

As defined generally above, each instance of R₁ is independently selected from the group consisting of hydrogen, halogen, —N₃, —CN, —NO₂, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, —OR^(A), —N(R^(B))₂, —SR^(A), —C(═O)R^(A), —C(═O)OR^(A), —C(═O)SR^(A), —C(═O)N(R^(B))₂, —C(═O)N(R^(B))N(R^(B))₂, —OC(═O)R^(A), —OC(═O)N(R^(B))₂, —NR^(B)C(═O)R^(A), —NR^(B)C(═O)N(R^(B))₂, —NR^(B)C(═O)N(R^(B))N(R^(B))₂, —NR^(B)C(═O)OR^(A), —SC(═O)R^(A), —C(═NR^(B))R^(A), —C(═NNR^(B))R^(A), —C(═NOR^(A))R^(A), —C(═NR^(B))N(R^(B))₂, —NR^(B)C(═NR^(B))R^(B), —C(═S)R^(A), —C(═S)N(R^(B))₂, —NR^(B)C(═S)R^(A), —S(═O)R^(A), —OS(═O)₂R^(A), —SO₂R^(A), —NR^(B)SO₂R^(A), or —SO₂N(R^(B))₂. In certain embodiments, R₁ is hydrogen. In some embodiments, R₁ is not hydrogen. In some embodiments, R₁ is halogen. In certain embodiments, R₁ is F. In certain embodiments, R₁ is Cl. In certain embodiments, R₁ is Br. In certain embodiments, R₁ is I. In some embodiments, R₁ is optionally substituted alkyl. In some embodiments, R₁ is optionally substituted alkenyl. In certain embodiments, R₁ is optionally substituted alkynyl. In certain embodiments, R₁ is optionally substituted C₁₋₆ alkyl. In certain embodiments, R₁ is substituted C₁₋₆ alkyl. In certain embodiments, R₁ is —CF₃, CHF₂, or CH₂F. In certain embodiments, R₁ is —C₁₋₆ alkyl-carbocyclyl. In certain embodiments, R₁ is —CH₂-cyclopropyl or —CH₂-cyclobutyl. In certain embodiments, R₁ is unsubstituted C₁₋₆ alkyl. In certain embodiments, R₁ is methyl, ethyl, propyl, butyl, or pentyl. In certain embodiments, R₁ is isopropyl, isobutyl, or isopentyl. In certain embodiments, R₁ is isobutyl. In some embodiments, R₁ is —CN. In some embodiments, R₁ is optionally substituted carbocyclyl, optionally substituted phenyl, optionally substituted heterocyclyl, or optionally substituted heteroaryl. In certain embodiments, R₁ is —N(R^(B))₂. In certain embodiments, R₁ is —NHR^(B). In certain embodiments, R₁ is —NH₂. In certain embodiments, R₁ is —OR^(A). In certain embodiments, R₁ is —OH. In certain embodiments, R₁ is —OR^(A), wherein R^(A) is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl. In certain embodiments, R₁ is —O— isobutylenyl. In certain embodiments, R₁ is —OR^(A), wherein R^(A) is optionally substituted C₁₋₆ alkyl. In certain embodiments, R₁ is —OR^(A), wherein R^(A) is unsubstituted C₁₋₆ alkyl. In certain embodiments, R₁ is —O-propyl, —O-isopropyl, —O-isobutyl, or —O-isopentyl. In certain embodiments, R₁ is —OR^(A), wherein R^(A) is substituted C₁₋₆ alkyl. In certain embodiments, R₁ is —O—C₁₋₆alkyl-O—C₁₋₆alkyl. In certain embodiments, R₁ is —OCH₂CH₂OCH₃ or —OCH₂CH₂CH₂OCH₃. In certain embodiments, R₁ is —O—C₁₋₆alkyl-carbocyclyl. In certain embodiments, R₁ is —O—CH₂-cyclobutyl or —O—CH₂-cyclopropyl. In certain embodiments, R₁ is —O—C₁₋₆alkyl-heterocyclyl. In certain embodiments, R₁ is —O—CH₂-tetrahydropyranyl or —O—CH₂-oxetanyl. In certain embodiments, R₁ is —OR^(A), wherein R^(A) is optionally substituted heterocyclyl. In certain embodiments, R₁ is —O-tetrahydropyranyl or —O-oxetanyl. In certain embodiments, R₁ is —OR^(A), wherein R^(A) is optionally substituted aryl. In certain embodiments, R₁ is —O-phenyl. In certain embodiments, R₁ is —OR^(A), wherein R^(A) is optionally substituted heteroaryl.

In certain embodiments, R₁ is —Z—R₄, wherein Z is a bond, —O—, —S—, —NR^(B)—, NR^(B)C(═O)—, —C(═O)NR^(B)—, —OC(═O)NR^(B)—, —NR^(B)C(═O)O—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, trans-CR^(C)═CR^(C)—, cis-CR^(C)═CR^(C)—, —C≡C—, —OC(R^(cc))₂—, —C(R^(cc))₂O—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(B)—, —NR^(B)S(═O)₂—, or an optionally substituted C₁₋₈ hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NR^(B)—, —NR^(B)C(═O)—, —C(═O)NR^(B)—, —OC(═O)NR^(B)—, —NR^(B)C(═O)O—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(B)C(═S)—, —C(═S)NR^(B)—, trans-CR^(C)═CR^(C)—, cis-CR^(C)═CR^(C)—, —C≡C—, —OC(R^(cc))₂—, —C(R^(cc))₂O—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(B)—, —NR^(B)S(═O)₂—, wherein each instance of R^(C) is independently selected from the group consisting of hydrogen, halogen optionally substituted alkyl, optionally substituted alkenyl, optionally substituted carbocyclyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted heterocyclyl, and optionally substituted heteroaryl, or two R^(C) groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring; and R₄ is hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, —OR^(A), —N(R^(B))₂, —SR^(A), or an oxygen protecting group. In certain embodiments, Z is —O—. In certain embodiments, Z is optionally substituted C₁₋₈ hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NR^(B)—, —NR^(B)C(═O)—, —C(═O)NR^(B)—, OC(═O)NR^(B)—, —NR^(B)C(═O)O—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(B) C(═S)—, —C(═S)NR^(B)—, trans-CR^(C)═CR^(C)—, cis-CR^(C)═CR^(C)—, —C≡C—, —OC(R^(cc))₂—, —C(R^(cc))₂O—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(B)—, or —NR^(B)S(═O)₂—. In certain embodiments, Z is —(CH₂)_(n)O—, wherein n is 1, 2, 3, 4, 5, 6, 7, or 8. In certain embodiments, Z is —CH₂O—. In certain embodiments, Z is —(CH₂)₂O—. In certain embodiments, Z is —(CH₂)₃O—. In certain embodiments, Z is —(CH₂)₄O—. In certain embodiments, Z is —(CH₂)₅O—. In certain embodiments, Z is —(CH₂)₆O—. In certain embodiments, Z is —(CH₂)₇O—. In certain embodiments, Z is —(CH₂)₈O—. In certain embodiments, Z is optionally substituted alkylene. In certain embodiments, Z is —(CH₂)_(s)—, wherein s is 1, 2, 3, 4, 5, 6, 7, or 8. In certain embodiments, Z is —CH₂—. In certain embodiments, Z is —(CH₂)₂—. In certain embodiments, Z is —(CH₂)₃—. In certain embodiments, Z is —(CH₂)₄—. In certain embodiments, Z is —(CH₂)₅—. In certain embodiments, Z is —(CH₂)₆—. In certain embodiments, Z is —(CH₂)₇—. In certain embodiments, Z is —(CH₂)₈—. In certain embodiments, Z is —(CH₂)_(t)—C(═O)NR^(B)—, wherein t is 0, 1, 2, 3, 4, 5, 6, 7, or 8. In certain embodiments, Z is —C(═O)NR^(B)—. In certain embodiments, Z is —CH₂—C(═O)NR^(B)—. In certain embodiments, Z is —(CH₂)₂—C(═O)NR^(B)—. In certain embodiments, Z is —(CH₂)₃—C(═O)NR^(B)—. In certain embodiments, Z is —(CH₂)₄—C(═O)NR^(B)—. In certain embodiments, Z is —(CH₂)₅—C(═O)NR^(B)—. In certain embodiments, Z is —(CH₂)₆—C(═O)NR^(B)—. In certain embodiments, Z is —(CH₂)₇—C(═O)NR^(B)—. In certain embodiments, Z is —(CH₂)₈—C(═O)NR^(B)—. In certain embodiments, Z is —NR^(B)C(═O)—. In certain embodiments, Z is —S—. In certain embodiments, Z is —NR^(B)—. In certain embodiments, Z is —OC(═O)NR^(B)—. In certain embodiments, Z is —NR^(B)C(═O)O—. In certain embodiments, Z is —SC(═O)—. In certain embodiments, Z is —C(═O)S—. In certain embodiments, Z is —OC(═O)—. In certain embodiments, Z is —C(═O)O—. In certain embodiments, Z is —NR^(B)C(═S)—. In certain embodiments, Z is —C(═S)NR^(B)—. In certain embodiments, Z is trans-CR^(C)═CR^(C)—. In certain embodiments, Z is cis-CR^(C)═CR^(C)—. In certain embodiments, Z is —C≡C—. In certain embodiments, Z is —OC(R^(C))₂—. In certain embodiments, Z is —S(═O)₂O—. In certain embodiments, Z is —OS(═O)₂—. In certain embodiments, Z is —OS(═)₂—. In certain embodiments, Z is —S(═O)₂NR^(B)—. In certain embodiments, Z is —NR^(B)S(═O)₂—. In certain embodiments, R₄ is hydrogen. In some embodiments, R₄ is optionally substituted alkyl. In some embodiments, R₄ is optionally substituted alkenyl. In certain embodiments, R₄ is optionally substituted alkynyl. In certain embodiments, R₄ is optionally substituted C₁₋₆ alkyl. In certain embodiments, R₄ is substituted C₁₋₆ alkyl. In certain embodiments, R₄ is unsubstituted C₁₋₆ alkyl. In certain embodiments, R₄ is methyl, ethyl, propyl, butyl, pentyl, isopropyl, isobutyl, or isopentyl. In certain embodiments, R₄ is optionally substituted carbocyclyl. In certain embodiments, R₄ is optionally substituted cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl. In certain embodiments, R₄ is unsubstituted cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl. In certain embodiments, R₄ is of the formula

wherein R₅ is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl. In certain embodiments, R₅ is optionally substituted methyl, ethyl, propyl, butyl, pentyl, isopropyl, isobutyl, or isopentyl. In certain embodiments, R₅ is benzyl. In certain embodiments, R₅ is methyl, ethyl, propyl, butyl, pentyl, isopropyl, isobutyl, or isopentyl. In certain embodiments, R₅ is isopropyl. In certain embodiments, R₅ is optionally substituted aryl. In certain embodiments, R₅ is phenyl. In certain embodiments, R₄ is optionally substituted aryl. In certain embodiments, R₄ is optionally substituted heterocyclyl. In certain embodiments, R₄ is optionally substituted five-membered heterocyclyl. In certain embodiments, R₄ is optionally substituted six-membered heterocyclyl. In certain embodiments, R₄ is optionally substituted five-membered heteroaryl. In certain embodiments, R₄ is optionally substituted pyrrole, furan, thiophene, imidazole, pyrazole, isothiazole isoxazole, oxazole, thiazole, 1,2,3-oxadiazole, 1,2,3-thiadiazole, 1,2,4-oxadiazole, 1,2,4-thiadiazole, 1,2,5-oxadiazole, 1,2,5-thiadiazole, 1,2,3-triazole, 1,2,4-triazole, 1,3,4-oxadiazole, 1,3,4-thiadiazole, 1,2,3,4-oxatriazole, 1,2,3,5-oxatriazole, or 2H-tetrazole. In certain embodiments, R₄ is optionally substituted six-membered heteroaryl. In certain embodiments, R₄ is optionally substituted six-membered heteroaryl. In certain embodiments, R₄ is optionally substituted pyridine. In certain embodiments, R₄ is —OR^(A). In certain embodiments, R₄ is —OH. In certain embodiments, R₄ is —O-methyl, —O-ethyl, —O-propyl, —O-butyl, —O-isopropyl, or —O-isobutyl.

In certain embodiments, Z is —O— and R₄ is optionally substituted alkyl. In certain embodiments, Z is —O— and R₄ is optionally substituted carbocyclyl. In certain embodiments, Z is —O— and R₄ is optionally substituted aralkyl. In certain embodiments, Z is —O— and R₄ is optionally substituted benzyl. In certain embodiments, Z is —O— and R₄ is optionally unsubstituted benzyl. In certain embodiments, Z is —O— and R₄ is optionally substituted cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl. In certain embodiments, Z is —O— and R₄ is unsubstituted cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl. In certain embodiments, Z is —O— and R₄ is of the formula

In certain embodiments, Z is —(CH₂)_(n)O— and R₄ is optionally substituted alkyl. In certain embodiments, Z is —(CH₂)_(n)O— and R₄ is —OR^(A). In certain embodiments, Z is —(CH₂)_(n)O— and R₄ is —N(R^(B))₂. In certain embodiments, Z is —(CH₂)_(n)O— and R₄ is —SR^(A). In certain embodiments, Z is —(CH₂)_(n)O— and R₄ is optionally substituted six-membered heteroaryl. In certain embodiments, Z is —(CH₂)_(n)O— and R₄ is optionally substituted five-membered heteroaryl. In certain embodiments, Z is —(CH₂)_(n)O— and R₄ is optionally substituted six-membered heteroaryl. In certain embodiments, Z is —(CH₂)_(n)O— and R₄ is optionally substituted pyrazole. In certain embodiments, Z is —(CH₂)_(s)— and R₄ is optionally substituted pyridine. In certain embodiments, Z is —(CH₂)_(s)— and R₄ is optionally substituted six-membered heteroaryl. In certain embodiments, Z is —(CH₂)_(s)— and R₄ is optionally substituted five-membered heteroaryl. In certain embodiments, Z is —(CH₂)_(s)— and R₄ is optionally substituted six-membered heteroaryl. In certain embodiments, Z is —(CH₂)_(s)— and R₄ is optionally substituted pyrazole. In certain embodiments, Z is —(CH₂)_(s)— and R₄ is optionally substituted pyridine. In certain embodiments, Z is —(CH₂)_(t)—C(═O)NR^(B)— and R₄ is optionally substituted six-membered heteroaryl. In certain embodiments, Z is —(CH₂)_(t)—C(═O)NR^(B)— and R₄ is optionally substituted five-membered heteroaryl. In certain embodiments, Z is —(CH₂)_(t)—C(═O)NR^(B)— and R₄ is optionally substituted six-membered heteroaryl. In certain embodiments, Z is —(CH₂)_(t)—C(═O)NR^(B)— and R₄ is optionally substituted pyrazole. In certain embodiments, Z is —(CH₂)_(t)—C(═O)NR^(B)— and R₄ is optionally substituted pyridine. In certain embodiments, Z is —O— and R₄ is of the formula

In certain embodiments, R₄ is of the formula

wherein each of V₁, V₂, V₃, V₄, and V₅ is independently C or N. In certain embodiments, R₄ is of the formula

In certain embodiments, R₄ is of the formula

In certain embodiments, R₄ is of the formula

In certain embodiments, R₄ is of the formula

In certain embodiments, R₄ is of the formula

In certain embodiments, R₄ is of the formula

In certain embodiments, R₄ is Of the formula

In certain embodiments, R₄ is of the formula

In certain embodiments, R₄ is of the formula

In certain embodiments, R₄ is of the formula

In certain embodiments, R₄ is selected from the group consisting of

As used herein, p is 0, 1, 2, 3, 4, or 5 as valence permits. In some embodiments, p is 0. In some embodiments, p is 1. In some embodiments, p is 2. In some embodiments, p is 3. In some embodiments, p is 4. In some embodiments, p is 5. In certain embodiments, R₄ is of the formula

In certain embodiments, R₄ is of the formula

In certain embodiments, R₄ is of the formula

As used herein, q is 0, 1, or 2. In certain embodiments, q is 1. In certain embodiments, q is 2.

In certain embodiments, R₄ is of the formula

wherein each of A₁, A₂, A₃, A₄, and A₅ is independently —C(R₇)₂—, —O—, or —NR_(7n)—; and R₇ and R_(7n) are defined herein. In certain embodiments, no more than two of A₁, A₂, A₃, A₄, and A₅ are —O—, or —NR_(7n)—.

In certain embodiments, R₄ is of the formula

wherein each of A₁, A₂, A₃, and A₄ is independently —C(R₇)₂—, —O—, or —NR_(7n)—; and R₇ and R_(7n) are defined herein. In certain embodiments, no more than one of A₁, A₂, A₃, and A₄ is —O—, or —NR_(7n)—.

In certain embodiments, R₄ is of the formula

wherein each of A₁, A₂, A₃, and A₄ is independently —C(R₇)₂—, —O—, or —NR_(7n)—; and R₇ and R_(7n) are defined herein. In certain embodiments, no more than two of A₁, A₂, A₃, and A₄ are —O—, or —NR_(7n)—.

In certain embodiments, R₄ is of the formula

wherein each of A₁, A₂, and A₃ is independently —C(R₇)₂—, —O—, or —NR_(7n)—; and R₇ and R_(7n) are defined herein. In certain embodiments, no more than one of A₁, A₂, and A₃ is —O— or —NR_(7n)—.

In certain embodiments, R₄ is of the formula

wherein A is —C(R₇)₂—, —O—, or —NR_(7n)—; wherein i, R₇, and R_(7n) are defined herein. In certain embodiments, R₄ is of the formula

wherein i, R₇, and R_(7n) are defined herein.

As defined generally herein, each instance of R₇ is independently selected from the group consisting of hydrogen, halogen, —N₃, —CN, —NO₂, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, —OR^(A), —N(R^(B))₂, —SR^(A), —C(═O)R^(A), —C(═O)OR^(A), —C(═O)SR^(A), —C(═O)N(R^(B))₂, —C(═O)N(R^(B))N(R^(B))₂, —OC(═O)R^(A), —OC(═O)N(R^(B))₂, —NR^(B)C(═O)R^(A), —NR^(B)C(═O)N(R^(B))₂, —NR^(B)C(═O)N(R^(B))N(R^(B))₂, —NR^(B)C(═O)OR^(A), —SC(═O)R^(A), —C(═NR^(B))R^(A), —C(═NNR^(B))R^(A), —C(═NOR^(A))R^(A), —C(═NR^(B))N(R^(B))₂, —NR^(B)C(═NR^(B))R^(B), —C(═S)R^(A), —C(═S)N(R^(B))₂, —NR^(B)C(═S)R^(A), —S(═O)R^(A), —OS(═O)₂R^(A), —SO₂R^(A), —NR^(B)SO₂R^(A), and —SO₂N(R^(B))₂; or two R₇ groups can be joined to form an optionally substituted carbocyclic or heterocyclic ring. In certain embodiments, R₇ is hydrogen. In some embodiments, R₇ is not hydrogen. In some embodiments, R₇ is halogen. In certain embodiments, R₇ is F. In certain embodiments, R₇ is Cl. In certain embodiments, R₇ is Br. In certain embodiments, R₇ is I. In some embodiments, R₇ is optionally substituted alkyl. In some embodiments, R₇ is optionally substituted alkenyl. In certain embodiments, R₇ is optionally substituted alkynyl. In certain embodiments, R₇ is optionally substituted C₁₋₆ alkyl. In certain embodiments, R₇ is substituted C₁₋₆ alkyl. In certain embodiments, R₇ is —CF₃, CHF₂, or CH₂F. In certain embodiments, R₇ is —C₁₋₆ alkyl-carbocyclyl. In certain embodiments, R₇ is —CH₂-cyclopropyl or —CH₂-cyclobutyl. In certain embodiments, R₇ is unsubstituted C₁₋₆ alkyl. In certain embodiments, R₇ is methyl, ethyl, propyl, butyl, or pentyl. In certain embodiments, R₇ is isopropyl, isobutyl, or isopentyl. In certain embodiments, R₇ is isobutyl. In some embodiments, R₇ is —CN. In some embodiments, R₇ is optionally substituted carbocyclyl, optionally substituted phenyl, optionally substituted heterocyclyl, or optionally substituted heteroaryl. In certain embodiments, R₇ is —N(R^(B))₂. In certain embodiments, R₇ is —NHR^(B). In certain embodiments, R₇ is —NH₂. In certain embodiments, R₇ is —OR^(A). In certain embodiments, R₇ is —OH. In certain embodiments, R₇ is —OR^(A), wherein R^(A) is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl. In certain embodiments, R₇ is —O-isobutylenyl. In certain embodiments, R₇ is —OR^(A), wherein R^(A) is optionally substituted C₁₋₆ alkyl. In certain embodiments, R₇ is —OR^(A), wherein R^(A) is unsubstituted C₁₋₆ alkyl. In certain embodiments, R₇ is —O-methyl, —O-ethyl, —O-propyl, —O— butyl, —O-pentyl, —O-isopropyl, —O-isobutyl, or —O-isopentyl. In certain embodiments, two R₇ groups are joined to form an optionally substituted carbocyclic ring. In certain embodiments, two R₇ groups are joined to form an optionally substituted heterocyclic ring.

As defined generally herein, each instance of R_(7n) is independently selected from the group consisting of hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, and a nitrogen protecting group. In certain embodiments, R_(7n) is hydrogen. In certain embodiments, R_(7n) is optionally substituted acyl. In certain embodiments, R_(7n) is optionally substituted alkyl. In certain embodiments, R_(7n) is optionally substituted C₁₋₆ alkyl. In certain embodiments, R_(7n) is substituted C₁₋₆ alkyl. In certain embodiments, R_(7n) is unsubstituted C₁₋₆ alkyl. In certain embodiments, R_(7n) is methyl, ethyl, propyl, butyl, pentyl, isopropyl, isobutyl, or isopentyl. In certain embodiments, R_(7n) is optionally substituted alkenyl. In certain embodiments, R_(7n) is optionally substituted alkynyl. In certain embodiments, R_(7n) is optionally substituted carbocyclyl. In certain embodiments, R_(7n) is optionally substituted aryl. In certain embodiments, R_(7n) is optionally substituted heterocyclyl. In certain embodiments, R_(7n) is optionally substituted heteroaryl. In certain embodiments, R_(7n) is optionally substituted alkyl-Cy. In certain embodiments, R_(7n) is a nitrogen protecting group.

As defined generally herein, i is 0, 1, 2, 3, 4, 5, 6, 7, or 8, as valency permits. In certain embodiments, i is 0. In certain embodiments, i is 1. In certain embodiments, i is 2. In certain embodiments, i is 3. In certain embodiments, i is 4. In certain embodiments, i is 5. In certain embodiments, i is 6. In certain embodiments, i is 7. In certain embodiments, i is 8.

As described herein, each instance of R₆ is independently selected from the group consisting of hydrogen, halogen, —N₃, —CN, —NO₂, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, —OR^(A), —N(R^(B))₂, —SR^(A), —C(═O)R^(A), —C(═O)OR^(A), —C(═O)SR^(A), —C(═O)N(R^(B))₂, —C(═O)N(R^(B))N(R^(B))₂, —OC(═O)R^(A), —OC(═O)N(R^(B))₂, —NR^(B)C(═O)R^(A), —NR^(B)C(═O)N(R^(B))₂, —NR^(B)C(═O)N(R^(B))N(R^(B))₂, —NR^(B)C(═O)OR^(A), —SC(═O)R^(A), —C(═NR^(B))R^(A), —C(═NNR^(B))R^(A), —C(═NOR^(A))R^(A), —C(═NR^(B))N(R^(B))₂, —NR^(B)C(═NR^(B))R^(B), —C(═S)R^(A), —C(═S)N(R^(B))₂, —NR^(B)C(═S)R^(A), —S(═O)R^(A), —OS(═O)₂R^(A), —SO₂R^(A), —NR^(B)SO₂R^(A), or —SO₂N(R^(B))₂. In certain embodiments, R₆ is hydrogen. In some embodiments, R₆ is not hydrogen. In some embodiments, R₆ is halogen. In certain embodiments, R₆ is F. In certain embodiments, R₆ is Cl. In certain embodiments, R₆ is Br. In certain embodiments, R₆ is I. In some embodiments, R₆ is optionally substituted alkyl. In some embodiments, R₆ is optionally substituted alkenyl. In certain embodiments, R₆ is optionally substituted alkynyl. In certain embodiments, R₆ is optionally substituted C₁₋₆ alkyl. In certain embodiments, R₆ is substituted C₁₋₆ alkyl. In certain embodiments, R₆ is —CF₃, CHF₂, or CH₂F. In certain embodiments, R₆ is —C₁₋₆ alkyl-carbocyclyl. In certain embodiments, R₆ is —CH₂-cyclopropyl or —CH₂-cyclobutyl. In certain embodiments, R₆ is unsubstituted C₁₋₆ alkyl. In certain embodiments, R₆ is methyl, ethyl, propyl, butyl, or pentyl. In certain embodiments, R₆ is isopropyl, isobutyl, or isopentyl. In certain embodiments, R₁ is isobutyl. In some embodiments, R₆ is —CN. In some embodiments, R₆ is optionally substituted carbocyclyl, optionally substituted phenyl, optionally substituted heterocyclyl, or optionally substituted heteroaryl. In certain embodiments, R₆ is —N(R^(B))₂. In certain embodiments, R₆ is —NHR^(B). In certain embodiments, R₁ is —NH₂. In certain embodiments, R₆ is —OR^(A). In certain embodiments, R₆ is —OH. In certain embodiments, R₆ is —OR^(A), wherein R^(A) is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl. In certain embodiments, R₆ is —O— isobutylenyl. In certain embodiments, R₆ is —OR^(A), wherein R^(A) is optionally substituted C₁₋₆ alkyl. In certain embodiments, R₆ is —OR^(A), wherein R^(A) is unsubstituted C₁₋₆ alkyl. In certain embodiments, R₆ is —O-methyl, —O-ethyl, —O-propyl, —O-butyl, —O-pentyl, —O-isopropyl, —O— isobutyl, or —O-isopentyl.

As defined generally above, R₂ is hydrogen, optionally substituted C₁₋₆ alkyl, optionally substituted C₂₋₆ alkenyl, optionally substituted C₂₋₆ alkynyl, optionally substituted C₃₋₇ cycloalkyl, optionally substituted 4- to 7-membered heterocyclyl; or optionally substituted C₁₋₄ alkyl-Cy, wherein Cy is optionally substituted C₃₋₇ cycloalkyl, optionally substituted 4- to 7-membered heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl. As defined generally above, each instance of Cy is independently optionally substituted C₃₋₇ cycloalkyl, optionally substituted 4- to 7-membered heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl. In some embodiments, Cy is optionally substituted C₃₋₇ cycloalkyl. In some embodiments, Cy is optionally substituted 4- to 7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some embodiments, Cy is oxetane, tetrahydrofuran, or tetrahydropyran. In some embodiments, Cy is optionally substituted aryl. In some embodiments, Cy is optionally substituted phenyl. In some embodiments, Cy is unsubstituted phenyl. In some embodiments, Cy is optionally substituted heteroaryl having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some embodiments, Cy is optionally substituted 5- to 6-membered heteroaryl having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur. In some embodiments, Cy is pyridyl. In some embodiments, R₂ is

In some embodiments, R₂ is

In some embodiments, R₂ is

In some embodiments, R₂ is

In some embodiments, R₂ is

As defined generally above, R₃ is hydrogen, C₁₋₄ alkyl, or C₃₋₄ cycloalkyl. In certain embodiments, R₃ is hydrogen. In certain embodiments, R₃ is C₁₋₄ alkyl. In certain embodiments, R₃ is methyl, ethyl, propyl, butyl, or pentyl. In certain embodiments, R₃ is isopropyl, isobutyl, or isopentyl. In certain embodiments, R₃ is isobutyl. In certain embodiments, R³ is C₃₋₄ cycloalkyl. In certain embodiments, R³ is cyclopropyl. In certain embodiments, R³ is cyclobutyl.

As defined generally above, R_(x) is optionally substituted C₁₋₄ alkyl or optionally substituted C₃₋₄ cycloalkyl. In certain embodiments, R_(x) is unsubstituted C₁₋₄ alkyl. In certain embodiments, R_(x) is methyl. In certain embodiments, R_(x) is ethyl. In certain embodiments, R_(x) is isopropyl. In certain embodiments, R_(x) is propyl. In certain embodiments, R_(x) is butyl. In certain embodiments, R_(x) is substituted C₁₋₄ alkyl. In certain embodiments, R_(x) is C₁₋₄ alkyl substituted with hydroxyl or alkoxy. In certain embodiments, R_(x) is hydroxyethyl or methoxyethyl. In certain embodiments, R_(x) is optionally substituted C₃₋₄ cycloalkyl. In certain embodiments, R_(x) is unsubstituted C₃₋₄ cycloalkyl. In certain embodiments, R_(x) is substituted cyclopropyl. In certain embodiments, R_(x) is unsubstituted cyclopropyl. In certain embodiments, R_(x) is substituted cyclobutyl. In certain embodiments, R_(x) is unsubstituted cyclobutyl.

As defined generally above, m is 0, 1, 2, 3, or 4. In certain embodiments, m is 0. In certain embodiments, m is 1. In certain embodiments, m is 2. In certain embodiments, m is 3. In certain embodiments, m is 4.

As defined generally above, each instance of R^(A) is independently selected from the group consisting of hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, an oxygen protecting group when attached to an oxygen atom, and a sulfur protecting group when attached to a sulfur atom. In certain embodiments, R^(A) is hydrogen. In certain embodiments, R^(A) is optionally substituted acyl. In certain embodiments, R^(A) is optionally substituted alkyl. In certain embodiments, R^(A) is optionally substituted C₁₋₆ alkyl. In certain embodiments, R^(A) is substituted C₁₋₆ alkyl. In certain embodiments, R^(A) is unsubstituted C₁₋₆ alkyl. In certain embodiments, R^(A) is methyl, ethyl, propyl, butyl, pentyl, isopropyl, isobutyl, or isopentyl. In certain embodiments, R^(A) is optionally substituted alkenyl. In certain embodiments, R^(A) is optionally substituted alkynyl. In certain embodiments, R^(A) is optionally substituted carbocyclyl. In certain embodiments, R^(A) is optionally substituted aryl. In certain embodiments, R^(A) is optionally substituted heterocyclyl. In certain embodiments, R^(A) is optionally substituted heteroaryl. In certain embodiments, R^(A) is optionally substituted alkyl-Cy. In certain embodiments, R^(A) is an oxygen protecting group. In certain embodiments, R^(A) is a sulfur protecting group.

As defined generally above, each instance of R^(B) is independently selected from the group consisting of hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, and a nitrogen protecting group, or two R^(B) groups are taken together with their intervening atoms to form an optionally substituted heterocyclic ring. In certain embodiments, R^(B) is hydrogen. In certain embodiments, R^(B) is optionally substituted acyl. In certain embodiments, R^(B) is optionally substituted alkyl. In certain embodiments, R^(B) is optionally substituted C₁₋₆ alkyl. In certain embodiments, R^(B) is substituted C₁₋₆ alkyl. In certain embodiments, R^(B) is unsubstituted C₁₋₆ alkyl. In certain embodiments, R^(B) is methyl, ethyl, propyl, butyl, pentyl, isopropyl, isobutyl, or isopentyl. In certain embodiments, R^(B) is optionally substituted alkenyl. In certain embodiments, R^(B) is optionally substituted alkynyl. In certain embodiments, R^(B) is optionally substituted carbocyclyl. In certain embodiments, R^(B) is optionally substituted aryl. In certain embodiments, R^(B) is optionally substituted heterocyclyl. In certain embodiments, R^(B) is optionally substituted heteroaryl. In certain embodiments, R^(B) is optionally substituted alkyl-Cy. In certain embodiments, R^(B) is a nitrogen protecting group. In certain embodiments, two R^(B) groups are taken together with their intervening atoms to form an optionally substituted heterocyclic ring.

As generally defined herein each of A₁, A₂, A₃, A₄, and A₅ is independently —C(R₇)₂—, —O—, or —NR_(7n)—; and R₇ and R_(7n) are defined herein. In certain embodiments, no more than two of A₁, A₂, A₃, A₄, and A₅ are —O—, or —NR_(7n)—. In certain embodiments, no more than one of A₁, A₂, A₃, A₄, and A₅ are —O—, or —NR_(7n)—. In certain embodiments, A is —CH₂—. In certain embodiments, A₁ is —O—. In certain embodiments, A is —NR_(7n)—. In certain embodiments, A₂ is —CH₂—. In certain embodiments, A₂ is —O—. In certain embodiments, A₂ is —NR_(7n)—. In certain embodiments, A₃ is —CH₂—. In certain embodiments, A₃ is —O—. In certain embodiments, A₃ is —NR_(7n)—. In certain embodiments, A₄ is —CH₂—. In certain embodiments, A₄ is —O—. In certain embodiments, A₄ is —NR_(7n)—. In certain embodiments, A₅ is —CH₂—. In certain embodiments, A₅ is —O—. In certain embodiments, A₅ is —NR_(7n)—. In certain embodiments, A₁ is —CH₂—; and A₂, A₃, A₄, and A₅ are —CH₂—. In certain embodiments, A₁ is —O—; and A₂, A₃, A₄, and A₅ are —CH₂—. In certain embodiments, A is —NR_(7n)—; and A₂, A₃, A₄, and A₅ are —CH₂—. In certain embodiments, A₂ is —CH₂—; and A₁, A₃, A₄, and A₅ are —CH₂—. In certain embodiments, A₂ is —O—; and A₁, A₃, A₄, and A₅ are —CH₂—. In certain embodiments, A₂ is —NR_(7n)—; and A₁, A₃, A₄, and A₅ are —CH₂—. In certain embodiments, A₃ is —CH₂—; and A₂, A₁, A₄, and A₅ are —CH₂—. In certain embodiments, A₃ is —O—; and A₂, A₁, A₄, and A₅ are —CH₂—. In certain embodiments, A₃ is —NR_(7n)—; and A₂, A₁, A₄, and A₅ are —CH₂—. In certain embodiments, A₄ is —CH₂—; and A₂, A₃, A₁, and A₅ are —CH₂—. In certain embodiments, A₄ is —O—; and A₂, A₃, A₁, and A₅ are —CH₂—. In certain embodiments, A₄ is —NR_(7n)—; and A₂, A₃, A₁, and A₅ are —CH₂—. In certain embodiments, A₅ is —CH₂—; and A₂, A₃, A₄, and A₁ are —CH₂—. In certain embodiments, A₅ is —O—; and A₂, A₃, A₄, and A₁ are —CH₂—. In certain embodiments, A₅ is —NR_(7n)—; and A₂, A₃, A₄, and A are —CH₂—. In certain embodiments A₁ is —C(R₇)₂—; A₂, A₃, A₄, and A₅ are —CH₂—; and two R₇ groups are joined to form an optionally substituted carbocyclic or heterocyclic ring. In certain embodiments A₁ is —C(R₇)₂—; A₂, A₃, A₄, and A₅ are —CH₂—; and two R₇ groups are joined to form an unsubstituted carbocyclic ring. In certain embodiments A is —C(R₇)₂—; A₂, A₃, A₄, and A₅ are —CH₂—; and two R₇ groups are joined to form an unsubstituted cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl ring.

In certain embodiments, a provided compound is a compound listed in Table 1A or Table 1B, or a pharmaceutically acceptable salt thereof.

TABLE 1A Exemplary Compounds Cmpd LC-MS m/z No Stucture (M + H) lA

—  2

277.1  3

305.1  4

305.1  5

293.0  6

307.1  7

339.1  8

305.1  9

353.1 10

311.1 11

303.1 12

326.1 13

350.1 14

350.1 15

326.1 16

326.1 17

315.1

TABLE 1B Exemplary Compounds Cmpd LC-MS m/z No Stucture (M + H) 1B

311.2 18

250.28 19

235.5 20

336.26 21

475.62 22

379.38 23

323.07 24

337 25

261.2 26

370 27

303.1 28

301.24 29

301.9 30

301.1 31

299.1 32

379.48 33

333.41 34

374.48 35

317.45 36

434.56 37

332.4 38

325.36 39

369.33 40

345.27 41

360.1 42

341.42 43

326.4 44

369.38 45

392.5 46

263.32 47

278.38 48

277.38 49

368.43 50

369.23 51

393.39 52

368.38 53

382.34 54

381.28 55

393.44 56

368.28 57

382.49 58

250.28 59

235.5 60

336.26 61

475.62 62

379.38 63

323.07 64

337 65

261.2 66

370 67

303.1 68

301.24 69

301.9 70

301.1 71

299.1 72

379.48 73

333.41 74

374.48

In certain embodiments, a provided compound inhibits an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8). In certain embodiments, a provided compound inhibits wild-type PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8. In certain embodiments, a provided compound inhibits a mutant RMT. In certain embodiments, a provided compound inhibits PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8, e.g., as measured in an assay described herein. In certain embodiments, the RMT is from a human. In certain embodiments, a provided compound inhibits an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8) at an IC₅₀ less than or equal to 10 μM. In certain embodiments, a provided compound inhibits an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8) at an IC₅₀ less than or equal to 1 μM. In certain embodiments, a provided compound inhibits an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8) at an IC₅₀ less than or equal to 0.1 μM. In certain embodiments, a provided compound inhibits an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8) at an IC₅₀ less than or equal to 0.01 μM. In certain embodiments, a provided compound inhibits an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8) in a cell at an EC₃₀ less than or equal to 10 μM. In certain embodiments, a provided compound inhibits an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8) in a cell at an EC₃₀ less than or equal to 12 μM. In certain embodiments, a provided compound inhibits an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8) in a cell at an EC₃₀ less than or equal to 3 μM. In certain embodiments, a provided compound inhibits PRMT1 in a cell at an EC₃₀ less than or equal to 12 μM. In certain embodiments, a provided compound inhibits PRMT1 in a cell at an EC₃₀ less than or equal to 3 μM. In certain embodiments, a provided compound inhibits an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8) in a cell at an EC₃₀ less than or equal to 1 μM. In certain embodiments, a provided compound inhibits an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8) in a cell at an EC₃₀ less than or equal to 0.1 μM. In certain embodiments, a provided compound inhibits cell proliferation at an EC₅₀ less than or equal to 10 μM. In certain embodiments, a provided compound inhibits cell proliferation at an EC₅₀ less than or equal to 1 μM. In certain embodiments, a provided compound inhibits cell proliferation at an EC₅₀ less than or equal to 0.1 μM.

It will be understood by one of ordinary skill in the art that the RMT can be wild-type, or any mutant or variant.

The present disclosure provides pharmaceutical compositions comprising a compound described herein, e.g., a compound of Formula (I), or a pharmaceutically acceptable salt thereof, as described herein, and optionally a pharmaceutically acceptable excipient. It will be understood by one of ordinary skill in the art that the compounds described herein, or salts thereof, may be present in various forms, such as amorphous, hydrates, solvates, or polymorphs. In certain embodiments, a provided composition comprises two or more compounds described herein. In certain embodiments, a compound described herein, or a pharmaceutically acceptable salt thereof, is provided in an effective amount in the pharmaceutical composition. In certain embodiments, the effective amount is a therapeutically effective amount. In certain embodiments, the effective amount is an amount effective for inhibiting an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8). In certain embodiments, the effective amount is an amount effective for treating an RMT-mediated disorder (e.g., a PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8-mediated disorder). In certain embodiments, the effective amount is a prophylactically effective amount. In certain embodiments, the effective amount is an amount effective to prevent an RMT-mediated disorder.

Pharmaceutically acceptable excipients include any and all solvents, diluents, or other liquid vehicles, dispersions, suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants, and the like, as suited to the particular dosage form desired. General considerations in formulation and/or manufacture of pharmaceutical compositions agents can be found, for example, in Remington's Pharmaceutical Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980), and Remington: The Science and Practice of Pharmacy, 21st Edition (Lippincott Williams & Wilkins, 2005).

Pharmaceutical compositions described herein can be prepared by any method known in the art of pharmacology. In general, such preparatory methods include the steps of bringing a compound described herein (the “active ingredient”) into association with a carrier and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit.

Pharmaceutical compositions can be prepared, packaged, and/or sold in bulk, as a single unit dose, and/or as a plurality of single unit doses. As used herein, a “unit dose” is discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient. The amount of the active ingredient is generally equal to the dosage of the active ingredient which would be administered to a subject and/or a convenient fraction of such a dosage such as, for example, one-half or one-third of such a dosage.

Relative amounts of the active ingredient, the pharmaceutically acceptable excipient, and/or any additional ingredients in a pharmaceutical composition of the present disclosure will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered. By way of example, the composition may comprise between 0.1% and 100% (w/w) active ingredient.

In some embodiments, a pharmaceutical composition described herein is sterilized.

Pharmaceutically acceptable excipients used in the manufacture of provided pharmaceutical compositions include inert diluents, dispersing and/or granulating agents, surface active agents and/or emulsifiers, disintegrating agents, binding agents, preservatives, buffering agents, lubricating agents, and/or oils. Excipients such as cocoa butter and suppository waxes, coloring agents, coating agents, sweetening, flavoring, and perfuming agents may also be present in the composition.

Exemplary diluents include calcium carbonate, sodium carbonate, calcium phosphate, dicalcium phosphate, calcium sulfate, calcium hydrogen phosphate, sodium phosphate lactose, sucrose, cellulose, microcrystalline cellulose, kaolin, mannitol, sorbitol, inositol, sodium chloride, dry starch, cornstarch, powdered sugar, and mixtures thereof.

Exemplary granulating and/or dispersing agents include potato starch, corn starch, tapioca starch, sodium starch glycolate, clays, alginic acid, guar gum, citrus pulp, agar, bentonite, cellulose and wood products, natural sponge, cation-exchange resins, calcium carbonate, silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone) (crospovidone), sodium carboxymethyl starch (sodium starch glycolate), carboxymethyl cellulose, cross-linked sodium carboxymethyl cellulose (croscarmellose), methylcellulose, pregelatinized starch (starch 1500), microcrystalline starch, water insoluble starch, calcium carboxymethyl cellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate, quaternary ammonium compounds, and mixtures thereof.

Exemplary surface active agents and/or emulsifiers include natural emulsifiers (e.g., acacia, agar, alginic acid, sodium alginate, tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidal clays (e.g., bentonite (aluminum silicate) and Veegum (magnesium aluminum silicate)), long chain amino acid derivatives, high molecular weight alcohols (e.g., stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetin monostearate, ethylene glycol distearate, glyceryl monostearate, and propylene glycol monostearate, polyvinyl alcohol), carbomers (e.g., carboxy polymethylene, polyacrylic acid, acrylic acid polymer, and carboxyvinyl polymer), carrageenan, cellulosic derivatives (e.g., carboxymethylcellulose sodium, powdered cellulose, hydroxymethyl cellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, methylcellulose), sorbitan fatty acid esters (e.g., polyoxyethylene sorbitan monolaurate (Tween 20), polyoxyethylene sorbitan (Tween 60), polyoxyethylene sorbitan monooleate (Tween 80), sorbitan monopalmitate (Span 40), sorbitan monostearate (Span 60], sorbitan tristearate (Span 65), glyceryl monooleate, sorbitan monooleate (Span 80)), polyoxyethylene esters (e.g., polyoxyethylene monostearate (Myrj 45), polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil, polyoxymethylene stearate, and Solutol), sucrose fatty acid esters, polyethylene glycol fatty acid esters (e.g., Cremophor™), polyoxyethylene ethers, (e.g., polyoxyethylene lauryl ether (Brij 30)), poly(vinyl-pyrrolidone), diethylene glycol monolaurate, triethanolamine oleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyl laurate, sodium lauryl sulfate, Pluronic F68, Poloxamer 188, cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride, docusate sodium, and/or mixtures thereof.

Exemplary binding agents include starch (e.g., cornstarch and starch paste), gelatin, sugars (e.g., sucrose, glucose, dextrose, dextrin, molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums (e.g., acacia, sodium alginate, extract of Irish moss, panwar gum, ghatti gum, mucilage of isapol husks, carboxymethylcellulose, methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, microcrystalline cellulose, cellulose acetate, poly(vinyl-pyrrolidone), magnesium aluminum silicate (Veegum), and larch arabogalactan), alginates, polyethylene oxide, polyethylene glycol, inorganic calcium salts, silicic acid, polymethacrylates, waxes, water, alcohol, and/or mixtures thereof.

Exemplary preservatives include antioxidants, chelating agents, antimicrobial preservatives, antifungal preservatives, alcohol preservatives, acidic preservatives, and other preservatives.

Exemplary antioxidants include alpha tocopherol, ascorbic acid, acorbyl palmitate, butylated hydroxyanisole, butylated hydroxytoluene, monothioglycerol, potassium metabisulfite, propionic acid, propyl gallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, and sodium sulfite.

Exemplary chelating agents include ethylenediaminetetraacetic acid (EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodium edetate, trisodium edetate, calcium disodium edetate, dipotassium edetate, and the like), citric acid and salts and hydrates thereof (e.g., citric acid monohydrate), fumaric acid and salts and hydrates thereof, malic acid and salts and hydrates thereof, phosphoric acid and salts and hydrates thereof, and tartaric acid and salts and hydrates thereof. Exemplary antimicrobial preservatives include benzalkonium chloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide, cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol, chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea, phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate, propylene glycol, and thimerosal.

Exemplary antifungal preservatives include butyl paraben, methyl paraben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoic acid, potassium benzoate, potassium sorbate, sodium benzoate, sodium propionate, and sorbic acid.

Exemplary alcohol preservatives include ethanol, polyethylene glycol, phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate, and phenylethyl alcohol.

Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E, beta-carotene, citric acid, acetic acid, dehydroacetic acid, ascorbic acid, sorbic acid, and phytic acid.

Other preservatives include tocopherol, tocopherol acetate, deteroxime mesylate, cetrimide, butylated hydroxyanisol (BHA), butylated hydroxytoluened (BHT), ethylenediamine, sodium lauryl sulfate (SLS), sodium lauryl ether sulfate (SLES), sodium bisulfite, sodium metabisulfite, potassium sulfite, potassium metabisulfite, Glydant Plus, Phenonip, methylparaben, Germall 115, Germaben II, Neolone, Kathon, and Euxyl. In certain embodiments, the preservative is an anti-oxidant. In other embodiments, the preservative is a chelating agent.

Exemplary buffering agents include citrate buffer solutions, acetate buffer solutions, phosphate buffer solutions, ammonium chloride, calcium carbonate, calcium chloride, calcium citrate, calcium glubionate, calcium gluceptate, calcium gluconate, D-gluconic acid, calcium glycerophosphate, calcium lactate, propanoic acid, calcium levulinate, pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasic calcium phosphate, calcium hydroxide phosphate, potassium acetate, potassium chloride, potassium gluconate, potassium mixtures, dibasic potassium phosphate, monobasic potassium phosphate, potassium phosphate mixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodium citrate, sodium lactate, dibasic sodium phosphate, monobasic sodium phosphate, sodium phosphate mixtures, tromethamine, magnesium hydroxide, aluminum hydroxide, alginic acid, pyrogen-free water, isotonic saline, Ringer's solution, ethyl alcohol, and mixtures thereof.

Exemplary lubricating agents include magnesium stearate, calcium stearate, stearic acid, silica, talc, malt, glyceryl behanate, hydrogenated vegetable oils, polyethylene glycol, sodium benzoate, sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate, sodium lauryl sulfate, and mixtures thereof.

Exemplary natural oils include almond, apricot kernel, avocado, babassu, bergamot, black current seed, borage, cade, camomile, canola, caraway, carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee, corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed, geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate, jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba, macademia nut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange, orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed, pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood, sasquana, savoury, sea buckthorn, sesame, shea butter, silicone, soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut, and wheat germ oils. Exemplary synthetic oils include, but are not limited to, butyl stearate, caprylic triglyceride, capric triglyceride, cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate, mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and mixtures thereof.

Liquid dosage forms for oral and parenteral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredients, the liquid dosage forms may comprise inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (e.g., cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents. In certain embodiments for parenteral administration, the compounds described herein are mixed with solubilizing agents such as Cremophor™, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and mixtures thereof.

Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions can be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation can be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that can be employed are water, Ringer's solution, U.S.P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.

The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.

In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This can be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility.

The rate of absorption of the drug then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle.

Compositions for rectal or vaginal administration are typically suppositories which can be prepared by mixing the compounds described herein with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.

Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active ingredient is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may comprise buffering agents.

Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes. Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.

The active ingredient can be in micro-encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active ingredient can be admixed with at least one inert diluent such as sucrose, lactose, or starch. Such dosage forms may comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets, and pills, the dosage forms may comprise buffering agents. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes.

Dosage forms for topical and/or transdermal administration of a provided compound may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants and/or patches. Generally, the active ingredient is admixed under sterile conditions with a pharmaceutically acceptable carrier and/or any desired preservatives and/or buffers as can be required. Additionally, the present disclosure encompasses the use of transdermal patches, which often have the added advantage of providing controlled delivery of an active ingredient to the body. Such dosage forms can be prepared, for example, by dissolving and/or dispensing the active ingredient in the proper medium. Alternatively or additionally, the rate can be controlled by either providing a rate controlling membrane and/or by dispersing the active ingredient in a polymer matrix and/or gel.

Formulations suitable for topical administration include, but are not limited to, liquid and/or semi liquid preparations such as liniments, lotions, oil in water and/or water in oil emulsions such as creams, ointments and/or pastes, and/or solutions and/or suspensions.

Topically-administrable formulations may, for example, comprise from about 1% to about 10% (w/w) active ingredient, although the concentration of the active ingredient can be as high as the solubility limit of the active ingredient in the solvent. Formulations for topical administration may further comprise one or more of the additional ingredients described herein.

A provided pharmaceutical composition can be prepared, packaged, and/or sold in a formulation suitable for pulmonary administration via the buccal cavity. Such a formulation may comprise dry particles which comprise the active ingredient and which have a diameter in the range from about 0.5 to about 7 nanometers or from about 1 to about 6 nanometers. Such compositions are conveniently in the form of dry powders for administration using a device comprising a dry powder reservoir to which a stream of propellant can be directed to disperse the powder and/or using a self propelling solvent/powder dispensing container such as a device comprising the active ingredient dissolved and/or suspended in a low-boiling propellant in a sealed container. Such powders comprise particles wherein at least 98% of the particles by weight have a diameter greater than 0.5 nanometers and at least 95% of the particles by number have a diameter less than 7 nanometers. Alternatively, at least 95% of the particles by weight have a diameter greater than 1 nanometer and at least 90% of the particles by number have a diameter less than 6 nanometers. Dry powder compositions may include a solid fine powder diluent such as sugar and are conveniently provided in a unit dose form.

Low boiling propellants generally include liquid propellants having a boiling point of below 65° F. at atmospheric pressure. Generally the propellant may constitute 50 to 99.9% (w/w) of the composition, and the active ingredient may constitute 0.1 to 20% (w/w) of the composition. The propellant may further comprise additional ingredients such as a liquid non-ionic and/or solid anionic surfactant and/or a solid diluent (which may have a particle size of the same order as particles comprising the active ingredient).

Pharmaceutical compositions formulated for pulmonary delivery may provide the active ingredient in the form of droplets of a solution and/or suspension. Such formulations can be prepared, packaged, and/or sold as aqueous and/or dilute alcoholic solutions and/or suspensions, optionally sterile, comprising the active ingredient, and may conveniently be administered using any nebulization and/or atomization device. Such formulations may further comprise one or more additional ingredients including, but not limited to, a flavoring agent such as saccharin sodium, a volatile oil, a buffering agent, a surface active agent, and/or a preservative such as methylhydroxybenzoate. The droplets provided by this route of administration may have an average diameter in the range from about 0.1 to about 200 nanometers.

Formulations described herein as being useful for pulmonary delivery are useful for intranasal delivery of a pharmaceutical composition. Another formulation suitable for intranasal administration is a coarse powder comprising the active ingredient and having an average particle from about 0.2 to 500 micrometers. Such a formulation is administered by rapid inhalation through the nasal passage from a container of the powder held close to the nares.

Formulations for nasal administration may, for example, comprise from about as little as 0.1% (w/w) and as much as 100% (w/w) of the active ingredient, and may comprise one or more of the additional ingredients described herein. A provided pharmaceutical composition can be prepared, packaged, and/or sold in a formulation for buccal administration. Such formulations may, for example, be in the form of tablets and/or lozenges made using conventional methods, and may contain, for example, 0.1 to 20% (w/w) active ingredient, the balance comprising an orally dissolvable and/or degradable composition and, optionally, one or more of the additional ingredients described herein. Alternately, formulations for buccal administration may comprise a powder and/or an aerosolized and/or atomized solution and/or suspension comprising the active ingredient. Such powdered, aerosolized, and/or aerosolized formulations, when dispersed, may have an average particle and/or droplet size in the range from about 0.1 to about 200 nanometers, and may further comprise one or more of the additional ingredients described herein.

A provided pharmaceutical composition can be prepared, packaged, and/or sold in a formulation for ophthalmic administration. Such formulations may, for example, be in the form of eye drops including, for example, a 0.1/1.0% (w/w) solution and/or suspension of the active ingredient in an aqueous or oily liquid carrier. Such drops may further comprise buffering agents, salts, and/or one or more other of the additional ingredients described herein. Other opthalmically-administrable formulations which are useful include those which comprise the active ingredient in microcrystalline form and/or in a liposomal preparation. Ear drops and/or eye drops are contemplated as being within the scope of this disclosure.

Although the descriptions of pharmaceutical compositions provided herein are principally directed to pharmaceutical compositions which are suitable for administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with ordinary experimentation.

Compounds provided herein are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of provided compositions will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular subject or organism will depend upon a variety of factors including the disease, disorder, or condition being treated and the severity of the disorder; the activity of the specific active ingredient employed; the specific composition employed; the age, body weight, general health, sex and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific active ingredient employed; the duration of the treatment; drugs used in combination or coincidental with the specific active ingredient employed; and like factors well known in the medical arts.

The compounds and compositions provided herein can be administered by any route, including enteral (e.g., oral), parenteral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal, topical (as by powders, ointments, creams, and/or drops), mucosal, nasal, bucal, sublingual; by intratracheal instillation, bronchial instillation, and/or inhalation; and/or as an oral spray, nasal spray, and/or aerosol. Specifically contemplated routes are oral administration, intravenous administration (e.g., systemic intravenous injection), regional administration via blood and/or lymph supply, and/or direct administration to an affected site. In general the most appropriate route of administration will depend upon a variety of factors including the nature of the agent (e.g., its stability in the environment of the gastrointestinal tract), and/or the condition of the subject (e.g., whether the subject is able to tolerate oral administration).

The exact amount of a compound required to achieve an effective amount will vary from subject to subject, depending, for example, on species, age, and general condition of a subject, severity of the side effects or disorder, identity of the particular compound(s), mode of administration, and the like. The desired dosage can be delivered three times a day, two times a day, once a day, every other day, every third day, every week, every two weeks, every three weeks, or every four weeks. In certain embodiments, the desired dosage can be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations).

In certain embodiments, an effective amount of a compound for administration one or more times a day to a 70 kg adult human may comprise about 0.0001 mg to about 3000 mg, about 0.0001 mg to about 2000 mg, about 0.0001 mg to about 1000 mg, about 0.001 mg to about 1000 mg, about 0.01 mg to about 1000 mg, about 0.1 mg to about 1000 mg, about 1 mg to about 1000 mg, about 1 mg to about 100 mg, about 10 mg to about 1000 mg, or about 100 mg to about 1000 mg, of a compound per unit dosage form.

In certain embodiments, a compound described herein may be administered at dosage levels sufficient to deliver from about 0.001 mg/kg to about 1000 mg/kg, from about 0.01 mg/kg to about mg/kg, from about 0.1 mg/kg to about 40 mg/kg, from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, or from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.

In some embodiments, a compound described herein is administered one or more times per day, for multiple days. In some embodiments, the dosing regimen is continued for days, weeks, months, or years.

It will be appreciated that dose ranges as described herein provide guidance for the administration of provided pharmaceutical compositions to an adult. The amount to be administered to, for example, a child or an adolescent can be determined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult.

It will be also appreciated that a compound or composition, as described herein, can be administered in combination with one or more additional therapeutically active agents. In certain embodiments, a compound or composition provided herein is administered in combination with one or more additional therapeutically active agents that improve its bioavailability, reduce and/or modify its metabolism, inhibit its excretion, and/or modify its distribution within the body. It will also be appreciated that the therapy employed may achieve a desired effect for the same disorder, and/or it may achieve different effects.

The compound or composition can be administered concurrently with, prior to, or subsequent to, one or more additional therapeutically active agents. In certain embodiments, the additional therapeutically active agent is a compound of Formula (I). In certain embodiments, the additional therapeutically active agent is not a compound of Formula (I). In general, each agent will be administered at a dose and/or on a time schedule determined for that agent. In will further be appreciated that the additional therapeutically active agent utilized in this combination can be administered together in a single composition or administered separately in different compositions. The particular combination to employ in a regimen will take into account compatibility of a provided compound with the additional therapeutically active agent and/or the desired therapeutic effect to be achieved. In general, it is expected that additional therapeutically active agents utilized in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.

Exemplary additional therapeutically active agents include, but are not limited to, small organic molecules such as drug compounds (e.g., compounds approved by the U.S. Food and Drug Administration as provided in the Code of Federal Regulations (CFR)), peptides, proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins, and cells. In certain embodiments, an additional therapeutically active agent is prednisolone, dexamethasone, doxorubicin, vincristine, mafosfamide, cisplatin, carboplatin, Ara-C, rituximab, azacitadine, panobinostat, vorinostat, everolimus, rapamycin, ATRA (all-trans retinoic acid), daunorubicin, decitabine, Vidaza, mitoxantrone, or IBET-151.

Also encompassed by the present disclosure are kits (e.g., pharmaceutical packs). The kits provided may comprise a provided pharmaceutical composition or compound and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container). In some embodiments, provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of a provided pharmaceutical composition or compound. In some embodiments, a provided pharmaceutical composition or compound provided in the container and the second container are combined to form one unit dosage form. In some embodiments, a provided kits further includes instructions for use.

Compounds and compositions described herein are generally useful for the inhibition of RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8). In some embodiments, methods of treating an RMT-mediated disorder in a subject are provided which comprise administering an effective amount of a compound described herein (e.g., a compound of Formula (I)), or a pharmaceutically acceptable salt thereof), to a subject in need of treatment. In certain embodiments, the effective amount is a therapeutically effective amount. In certain embodiments, the effective amount is a prophylactically effective amount. In certain embodiments, the subject is suffering from a RMT-mediated disorder. In certain embodiments, the subject is susceptible to a RMT-mediated disorder.

As used herein, the term “RMT-mediated disorder” means any disease, disorder, or other pathological condition in which an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8) is known to play a role. Accordingly, in some embodiments, the present disclosure relates to treating or lessening the severity of one or more diseases in which an RMT is known to play a role.

In some embodiments, the present disclosure provides a method of inhibiting an RMT comprising contacting the RMT with an effective amount of a compound described herein (e.g., a compound of Formula (I)), or a pharmaceutically acceptable salt thereof. The RMT may be purified or crude, and may be present in a cell, tissue, or subject. Thus, such methods encompass both inhibition of in vitro and in vivo RMT activity. In certain embodiments, the method is an in vitro method, e.g., such as an assay method. It will be understood by one of ordinary skill in the art that inhibition of an RMT does not necessarily require that all of the RMT be occupied by an inhibitor at once. Exemplary levels of inhibition of an RMT (e.g., PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8) include at least 10% inhibition, about 10% to about 25% inhibition, about 25% to about 50% inhibition, about 50% to about 75% inhibition, at least 50% inhibition, at least 75% inhibition, about 80% inhibition, about 90% inhibition, and greater than 90% inhibition.

In some embodiments, provided is a method of inhibiting RMT activity in a subject in need thereof (e.g., a subject diagnosed as having an RMT-mediated disorder) comprising administering to the subject an effective amount of a compound described herein (e.g., a compound of Formula (I)), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof.

In certain embodiments, provided is a method of modulating gene expression in a cell which comprises contacting a cell with an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof. In certain embodiments, the cell in culture in vitro. In certain embodiments, the cell is in an animal, e.g., a human. In certain embodiments, the cell is in a subject in need of treatment.

In certain embodiments, provided is a method of modulating transcription in a cell which comprises contacting a cell with an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof. In certain embodiments, the cell in culture in vitro. In certain embodiments, the cell is in an animal, e.g., a human. In certain embodiments, the cell is in a subject in need of treatment.

In certain embodiments, a method is provided of selecting a therapy for a subject having a disease associated with an RMT-mediated disorder or mutation comprising the steps of determining the presence of an RMT-mediated disorder or gene mutation in an RMT gene (e.g., a PRMT1, PRMT3, CARM1, PRMT6, and/or PRMT8 gene) or and selecting, based on the presence of an RMT-mediated disorder a gene mutation in the RMT gene a therapy that includes the administration of a provided compound. In certain embodiments, the disease is cancer.

In certain embodiments, a method of treatment is provided for a subject in need thereof comprising the steps of determining the presence of an RMT-mediated disorder or a gene mutation in the RMT gene and treating the subject in need thereof, based on the presence of a RMT-mediated disorder or gene mutation in the RMT gene with a therapy that includes the administration of a provided compound. In certain embodiments, the subject is a cancer patient.

In some embodiments, a compound provided herein is useful in treating a proliferative disorder, such as cancer. For example, while not being bound to any particular mechanism, protein arginine methylation by PRMTs is a modification that has been implicated in signal transduction, gene transcription, DNA repair and mRNA splicing, among others; and overexpression of PRMTs within these pathways is often associated with various cancers. Thus, compounds which inhibit the action of PRMTs, as provided herein, are effective in the treatment of cancer.

In some embodiments, compounds provided herein are effective in treating cancer through the inhibition of PRMT1. For example, PRMT1 overexpression has been observed in various human cancers, including, but not limited to, breast cancer, prostate cancer, lung cancer, colon cancer, bladder cancer, and leukemia. In one example, PRMT1 specifically deposits an asymmetric dimethylarginine (aDMA) mark on histone H4 at arginine 3 (H4R3me2a), and this mark is associated with transcription activation. In prostate cancer, the methylation status of H4R3 positively correlates with increasing tumor grade and can be used to predict the risk of prostate cancer recurrence (Seligson et al., Nature 2005 435, 1262-1266). Thus, in some embodiments, inhibitors of PRMT1, as described herein, are useful in treating cancers associated with the methylation status of H4R3, e.g., prostate cancer. Additionally, the methylarginine effector molecule TDRD3 interacts with the H4R3me2a mark, and overexpression of TDRD3 is linked to poor prognosis for the survival of patients with breast cancer (Nagahata et al., Cancer Sci. 2004 95, 218-225). Thus, in some embodiments, inhibitors of PRMT1, as described herein, are useful in treating cancers associated with overexpression of TDRD3, e.g., breast cancer, as inhibition of PRMT1 leads to a decrease in methylation of H4R3, thereby preventing the association of overexpressed TDRD3 with H4R3me2a. In other examples, PRMT1 is known to have non-histone substrates. For example, PRMT1, when localized to the cytoplasm, methylates proteins that are involved in signal transduction pathways, e.g., the estrogen receptor (ER). The expression status of ER in breast cancer is critical for prognosis of the disease, and both genomic and non-genomic ER pathways have been implicated in the pathogenesis of breast cancer. For example, it has been shown that PRMT1 methylates ERα, and that ERα methylation is required for the assembly of ERα with SRC (a proto-oncogene tyrosine-protein kinase) and focal adhesion kinase (FAK). Further, the silencing of endogenous PRMT1 resulted in the inability of estrogen to activate AKT. These results suggested that PRMT1-mediated ERα methylation is required for the activation of the SRC-PI3K-FAK cascade and AKT, coordinating cell proliferation and survival. Thus, hypermethylation of ERα in breast cancer is thought to cause hyperactivation of this signaling pathway, providing a selective survival advantage to tumor cells (Le Romancer et al., Mol. Cell 2008 31, 212-221; Le Romancer et al., Steroids 2010 75, 560-564). Accordingly, in some embodiments, inhibitors of PRMT1, as described herein, are useful in treating cancers associated with ERα methylation, e.g., breast cancer. In yet another example, PRMT1 has been shown to be involved in the regulation of leukemia development. For example, SRC-associated in mitosis 68 kDa protein (SAM68; also known as KHDRBS1) is a well-characterized PRMT1 substrate, and when either SAM68 or PRMT1 is fused directly to the myeloid/lymphoid leukemia (MLL) gene, these fusion proteins can activate MLL oncogenic properties, implying that the methylation of SAM68 by PRMT1 is a critical signal for the development of leukemia (Cheung et al., Nature Cell Biol. 2007 9, 1208-1215). Accordingly, in some embodiments, inhibitors of PRMT1, as described herein, are useful in treating cancers associated with SAM68 methylation, e.g., leukemia. In still another example, PRMT1 is implicated in leukemia development through its interaction with AE9a, a splice isoform of AML1-ETO (Shia et al., Blood 2012 119:4953-62). Knockdown of PRMT1 affects expression of certain AE9a-activated genes and suppresses AE9a's self-renewal capability. It has also been shown that AE9a recruits PRMT1 to AE9a activated gene promoters, which leads to increased H4 Arg3 methylation, H3 Lys9/14 acetylation, and transcription activated. Accordingly, in some embodiments, inhibitors of PRMT1, as described herein, are useful in treating cancers associated with AML1-ETO, e.g., leukemia. Thus, without being bound by any particular mechanism, the inhibition of PRMT1, e.g., by compounds described herein, is beneficial in the treatment of cancer.

In some embodiments, compounds provided herein are effective in treating cancer through the inhibition of PRMT3. In one example, the DAL1 tumor suppressor protein has been shown to interact with PRMT3 and inhibits its methyltransferase activity (Singh et al., Oncogene 2004 23, 7761-7771). Epigenetic downregulation of DAL1 has been reported in several cancers (e.g., meningiomas and breast cancer), thus PRMT3 is expected to display increased activity, and cancers that display DAL1 silencing may, in some aspects, be good targets for PRMT3 inhibitors, e.g., those described herein. Thus, without being bound by any particular mechanism, the inhibition of PRMT3, e.g., by compounds described herein, is beneficial in the treatment of cancer.

In some embodiments, compounds provided herein are effective in treating cancer through the inhibition of PRMT4, also known as CARM1. For example, PRMT4 levels have been shown to be elevated in castration-resistant prostate cancer (CRPC), as well as in aggressive breast tumors (Hong et al., Cancer 2004 101, 83-89; Majumder et al., Prostate 2006 66, 1292-1301). Thus, in some embodiments, inhibitors of PRMT4, as described herein, are useful in treating cancers associated with PRMT4 overexpression. PRMT4 has also been shown to affect ERα-dependent breast cancer cell differentiation and proliferation (Al-Dhaheri et al., Cancer Res. 2011 71, 2118-2128), thus in some aspects PRMT4 inhibitors, as described herein, are useful in treating ERα-dependent breast cancer by inhibiting cell differentiation and proliferation. In another example, PRMT4 has been shown to be recruited to the promoter of E2F1 (which encodes a cell cycle regulator) as a transcriptional co-activator (Frietze et al., Cancer Res. 2008 68, 301-306). Thus, PRMT4-mediated upregulation of E2F1 expression may contribute to cancer progression and chemoresistance as increased abundance of E2F1 triggers invasion and metastasis by activating growth receptor signaling pathways, which in turn promote an antiapoptotic tumor environment (Engelmann and Pützer, Cancer Res 2012 72; 571). Accordingly, in some embodiments, the inhibition of PRMT4, e.g., by compounds provided herein, is useful in treating cancers associated with E2F1 upregulation. Thus, without being bound by any particular mechanism, the inhibition of PRMT4, e.g., by compounds described herein, is beneficial in the treatment of cancer.

In some embodiments, compounds provided herein are effective in treating cancer through the inhibition of PRMT6. For example, PRMT6 has been reported to be overexpressed in a number of cancers, e.g., bladder and lung cancer (Yoshimatsu et al., Int. J. Cancer 2011 128, 562-573). Thus, in some embodiments, the inhibition of PRMT6, by compounds provided herein, is useful in treating cancers associated with PRMT6 overexpression. In some aspects, PRMT6 is primarily thought to function as a transcriptional repressor, although it has also been reported that PRMT6 functions as a co-activator of nuclear receptors. For example, as a transcriptional repressor, PRMT6 suppresses the expression of thrombospondin 1 (TSP1; also known as THBS1; a potent natural inhibitor of angiogenesis and endothelial cell migration) and p21 (a natural inhibitor of cyclin dependent kinase), thereby contributing to cancer development and progression (Michaud-Levesque and Richard, J. Biol. Chem. 2009 284, 21338-21346; Kleinschmidt et al., PLoS ONE 2012 7, e41446). Accordingly, in some embodiments, the inhibition of PRMT6, by compounds provided herein, is useful in treating cancer by preventing the repression of THBs1 and/or p21. Thus, without being bound by any particular mechanism, the inhibition of PRMT6, e.g., by compounds described herein, is beneficial in the treatment of cancer.

In some embodiments, compounds provided herein are effective in treating cancer through the inhibition of PRMT8. For example, deep-sequencing efforts of cancer genomes (e.g., COSMIC) have revealed that of all the PRMTs, PRMT8 is reported to be the most mutated. Of 106 sequenced genomes, 15 carry mutations in the PRMT8 coding region, and nine of these result in an amino acid change (Forbes et al., Nucleic Acids Res. 2011 39, D945-D950). Because of its high rate of mutation in cancer, PRMT8 is thought to contribute to the initiation or progression of cancer. Thus, without being bound by any particular mechanism, the inhibition of PRMT8, e.g., by compounds described herein, is beneficial in the treatment of cancer.

In some embodiments, compounds described herein are useful for treating a cancer including, but not limited to, acoustic neuroma, adenocarcinoma, adrenal gland cancer, anal cancer, angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma), appendix cancer, benign monoclonal gammopathy, biliary cancer (e.g., cholangiocarcinoma), bladder cancer, breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast), brain cancer (e.g., meningioma; glioma, e.g., astrocytoma, oligodendroglioma; medulloblastoma), bronchus cancer, carcinoid tumor, cervical cancer (e.g., cervical adenocarcinoma), choriocarcinoma, chordoma, craniopharyngioma, colorectal cancer (e.g., colon cancer, rectal cancer, colorectal adenocarcinoma), epithelial carcinoma, ependymoma, endotheliosarcoma (e.g., Kaposi's sarcoma, multiple idiopathic hemorrhagic sarcoma), endometrial cancer (e.g., uterine cancer, uterine sarcoma), esophageal cancer (e.g., adenocarcinoma of the esophagus, Barrett's adenocarinoma), Ewing sarcoma, eye cancer (e.g., intraocular melanoma, retinoblastoma), familiar hypereosinophilia, gall bladder cancer, gastric cancer (e.g., stomach adenocarcinoma), gastrointestinal stromal tumor (GIST), head and neck cancer (e.g., head and neck squamous cell carcinoma, oral cancer (e.g., oral squamous cell carcinoma (OSCC), throat cancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngeal cancer, oropharyngeal cancer)), hematopoietic cancers (e.g., leukemia such as acute lymphocytic leukemia (ALL) (e.g., B-cell ALL, T-cell ALL), acute myelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronic myelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), and chronic lymphocytic leukemia (CLL) (e.g., B-cell CLL, T-cell CLL); lymphoma such as Hodgkin lymphoma (HL) (e.g., B-cell HL, T-cell HL) and non-Hodgkin lymphoma (NHL) (e.g., B-cell NHL such as diffuse large cell lymphoma (DLCL) (e.g., diffuse large B-cell lymphoma (DLBCL)), follicular lymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), marginal zone B-cell lymphomas (e.g., mucosa-associated lymphoid tissue (MALT) lymphomas, nodal marginal zone B-cell lymphoma, splenic marginal zone B-cell lymphoma), primary mediastinal B-cell lymphoma, Burkitt lymphoma, lymphoplasmacytic lymphoma (e.g., “Waldenstrim's macroglobulinemia”), hairy cell leukemia (HCL), immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma and primary central nervous system (CNS) lymphoma; and T-cell NHL such as precursor T-lymphoblastic lymphoma/leukemia, peripheral T-cell lymphoma (PTCL) (e.g., cutaneous T-cell lymphoma (CTCL) (e.g., mycosis fungiodes, Sezary syndrome), angioimmunoblastic T-cell lymphoma, extranodal natural killer T-cell lymphoma, enteropathy type T-cell lymphoma, subcutaneous panniculitis-like T-cell lymphoma, anaplastic large cell lymphoma); a mixture of one or more leukemia/lymphoma as described above; and multiple myeloma (MM)), heavy chain disease (e.g., alpha chain disease, gamma chain disease, mu chain disease), hemangioblastoma, inflammatory myofibroblastic tumors, immunocytic amyloidosis, kidney cancer (e.g., nephroblastoma a.k.a. Wilms' tumor, renal cell carcinoma), liver cancer (e.g., hepatocellular cancer (HCC), malignant hepatoma), lung cancer (e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung), leiomyosarcoma (LMS), mastocytosis (e.g., systemic mastocytosis), myelodysplastic syndrome (MDS), mesothelioma, myeloproliferative disorder (MPD) (e.g., polycythemia Vera (PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a. myelofibrosis (MF), chronic idiopathic myelofibrosis, chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)), neuroblastoma, neurofibroma (e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis), neuroendocrine cancer (e.g., gastroenteropancreatic neuroendoctrine tumor (GEP-NET), carcinoid tumor), osteosarcoma, ovarian cancer (e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma), papillary adenocarcinoma, pancreatic cancer (e.g., pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors), penile cancer (e.g., Paget's disease of the penis and scrotum), pinealoma, primitive neuroectodermal tumor (PNT), prostate cancer (e.g., prostate adenocarcinoma), rectal cancer, rhabdomyosarcoma, salivary gland cancer, skin cancer (e.g., squamous cell carcinoma (SCC), keratoacanthoma (KA), melanoma, basal cell carcinoma (BCC)), small bowel cancer (e.g., appendix cancer), soft tissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor (MPNST), chondrosarcoma, fibrosarcoma, myxosarcoma), sebaceous gland carcinoma, sweat gland carcinoma, synovioma, testicular cancer (e.g., seminoma, testicular embryonal carcinoma), thyroid cancer (e.g., papillary carcinoma of the thyroid, papillary thyroid carcinoma (PTC), medullary thyroid cancer), urethral cancer, vaginal cancer and vulvar cancer (e.g., Paget's disease of the vulva).

In some embodiments, a compound provided herein is useful in treating diseases associated with increased levels of circulating asymmetric dimethylarginine (aDMA), e.g., cardiovascular disease, diabetes, kidney failure, renal disease, pulmonary disease, etc. Circulating aDMA is produced by the proteolysis of asymmetrically dimethylated proteins. PRMTs which mediate aDMA methylation include, e.g., PRMT1, PRMT3, PRMT4, PRMT6, and PRMT8. aDMA levels are directly involved in various diseases as aDMA is an endogenous competitive inhibitor of nitric oxide synthase (NOS), thereby reducing the production of nitric oxide (NO) (Vallance et al., J. Cardiovasc. Pharmacol. 1992 20 (Suppl. 12):S60-2). NO functions as a potent vasodilator in endothelial vessels, and as such inhibiting its production has major consequences on the cardiovascular system. For example, since PRMT1 is a major enzyme that generates aDMA, the dysregulation of its activity is likely to regulate cardiovascular diseases (Boger et al., Ann. Med. 2006 38:126-36), and other pathophysiological conditions such as diabetes mellitus (Sydow et al., Vasc. Med. 2005 10(Suppl. 1):S35-43), kidney failure (Vallance et al., Lancet 1992 339:572-5), and chronic pulmonary diseases (Zakrzewicz et al., BMC Pulm. Med. 2009 9:5). Additionally, it has been demonstrated that the expression of PRMT1 and PRMT3 are increased in coronary heart disease (Chen et al., Basic Res. Cardiol. 2006 101:346-53). In another example, aDMA elevation is seen in patients with renal failure, due to impaired clearance of this metabolite from the circulation (Jacobi et al., Am. J. Nephrol. 2008 28:224-37). Thus, circulating aDMA levels is observed in many pathophysiological situations. Accordingly, without being bound by any particular mechanism, the inhibition of PRMTs, e.g., by compounds described herein, results in the decrease of circulating aDMA, which is beneficial in the treatment of diseases associated with increased levels of circulating aDMA, e.g., cardiovascular disease, diabetes, kidney failure, renal disease, pulmonary disease, etc. In certain embodiments, a compound described herein is useful for treating or preventing vascular diseases.

In some embodiments, a compound provided herein is useful in treating metabolic disorders. For example, PRMT1 has been shown to enhance mRNA levels of FoxO1 target genes in gluconeogenesis, which results in increased hepatic glucose production, and knockdown of PRMT1 promotes inhibition of FoxO1 activity and thus inhibition of hepatic gluconeogenesis (Choi et al., Hepatology 2012 56:1546-56). Additionally, genetic haploinsufficiency of Prmt1 has been shown to reduce blood glucose levels in mouse models. Thus, without being bound by any particular mechanism, the inhibition of PRMT1, e.g., by compounds described herein, is beneficial in the treating of metabolic disorders, such as diabetes. In some embodiments, a provided compound is useful in treating type I diabetes. In some embodiments, a provided compound is useful in treating type II diabetes.

In some embodiments, a compound provided herein is useful in treating muscular dystrophies. For example, PRMT1, as well as PRMT3 and PRMT6, methylate the nuclear poly(A)-binding protein (PABPN1) in a region located near its C-terminus (Perreault et al., J. Biol. Chem. 2007 282:7552-62). This domain is involved in the aggregation of the PABPN1 protein, and abnormal aggregation of this protein is involved in the disease oculopharyngeal muscular dystrophy (Davies et al., Int. J. Biochem. Cell. Biol. 2006 38:1457-62). Thus, without being bound by any particular mechanism, the inhibition of PRMTs, e.g., by compounds described herein, is beneficial in the treatment of muscular dystrophies, e.g., oculopharyngeal muscular dystrophy, by decreasing the amount of methylation of PABPN1, thereby decreasing the amount of PABPN1 aggregation.

CARM1 is also the most abundant PRMT expressed in skeletal muscle cells, and has been found to selectively control the pathways modulating glycogen metabolism, and associated AMPK (AMP-activated protein kinase) and p38 MAPK (mitogen-activated protein kinase) expression. See, e.g., Wang et al., Biochem (2012) 444:323-331. Thus, in some embodiments, inhibitors of CARM1, as described herein, are useful in treating metabolic disorders, e.g., for example skeletal muscle metabolic disorders, e.g., glycogen and glucose metabolic disorders. Exemplary skeletal muscle metabolic disorders include, but are not limited to, Acid Maltase Deficiency (Glycogenosis type 2; Pompe disease), Debrancher deficiency (Glycogenosis type 3), Phosphorylase deficiency (McArdle's; GSD 5), X-linked syndrome (GSD9D), Autosomal recessive syndrome (GSD9B), Tarui's disease (Glycogen storage disease VII; GSD 7), Phosphoglycerate Mutase deficiency (Glycogen storage disease X; GSDX; GSD 10), Lactate dehydrogenase A deficiency (GSD 11), Branching enzyme deficiency (GSD 4), Aldolase A (muscle) deficiency, β-Enolase deficiency, Triosephosphate isomerase (TIM) deficiency, Lafora's disease (Progressive myoclonic epilepsy 2), Glycogen storage disease (Muscle, Type 0, Phosphoglucomutase 1 Deficiency (GSD 14)), and Glycogenin Deficiency (GSD 15).

In some embodiments, a compound provided herein is useful in treating autoimmune disease. For example, several lines of evidence strongly suggest that PRMT inhibitors may be valuable for the treatment of autoimmune diseases, e.g., rheumatoid arthritis. PRMTs are known to modify and regulate several critical immunomodulatory proteins. For example, post-translational modifications (e.g., arginine methylation), within T cell receptor signaling cascades allow T lymphocytes to initiate a rapid and appropriate immune response to pathogens. Co-engagement of the CD28 costimulatory receptor with the T cell receptor elevates PRMT activity and cellular protein arginine methylation, including methylation of the guanine nucleotide exchange factor Vavi (Blanchet et al., J. Exp. Med. 2005 202:371-377). PRMT inhibitors are thus expected to diminish methylation of the guanine exchange factor Vav1, resulting in diminished IL-2 production. In agreement, siRNA directed against PRMT5 was shown to both inhibit NFAT-driven promoter activity and IL-2 secretion (Richard et al., Biochem J. 2005 388:379-386). In another example, PRMT1 is known to cooperate with PRMT4 to enhance NFkB p65-driven transcription and facilitate the transcription of p65 target genes like TNFα (Covic et al., Embo. J. 2005 24:85-96). Thus, in some embodiments, PRMT1 and/or PRMT4 inhibitors, e.g., those described herein, are useful in treating autoimmune disease by decreasing the transcription of p65 target genes like TNFα. These examples demonstrate an important role for arginine methylation in inflammation. Thus, without being bound by any particular mechanism, the inhibition of PRMTs, e.g., by compounds described herein, is beneficial in the treatment of autoimmune diseases.

In some embodiments, a compound provided herein is useful in treating neurological disorders, such as amyotrophic lateral sclerosis (ALS). For example, a gene involved in ALS, TLS/FUS, often contains mutated arginines in certain familial forms of this disease (Kwiatkowski et al., Science 2009 323:1205-8). These mutants are retained in the cytoplasm, which is similar to reports documenting the role arginine methylation plays in nuclear-cytoplasmic shuffling (Shen et al., Genes Dev. 1998 12:679-91). This implicates PRMT, e.g., PRMT1, function in this disease, as it was demonstrated that TLS/FUS is methylated on at least 20 arginine residues (Rappsilber et al., Anal. Chem. 2003 75:3107-14). Thus, in some embodiments, the inhibition of PRMTs, e.g., by compounds provided herein, are useful in treating ALS by decreasing the amount of TLS/FUS arginine methylation.

In some embodiments, compounds of Formula (I) can be prepared using methods shown in Scheme 1. Scheme 1 shows a general synthesis route to indazole compounds of Formula (I), wherein R_(1′) and X′ are either the same as R₁ and X or are substituents which serve as precursors for synthetic conversion to R₁ and X wherein R₁, R_(x), R₃, X and Y are as defined above. In the first step indazole-3-carboxylates of general formula XI are reduced to alcohol intermediates of general formula XII using standard conditions, for example, using LiAlH₄ in THF under cooling or at room temperature. Intermediates XII can then be converted to indazole-3-carboxaldehydes of general formula XIII by oxidation using standard conditions, for example, using MnO₂ in an aprotic solvent at room or elevated temperature. Reaction of intermediates XIII with mono-Boc protected ethylenediamines of general formula XIV under reductive amination conditions (e.g. sodium cyanoborohydride and catalytic acid such as acetic acid) in an appropriate solvent (e.g. methanol) allows the preparation of intermediates of general formula XV. In a subsequent optional step or steps, either R_(1′) and X′ can be converted as required to the R₁ and X or substituents present in final compounds of Formula (I). For example, compounds with R₁ as an alkoxy group can be synthesized by deprotection of the alkylation intermediates of formula XV (e.g. deprecation of R_(1′)=OTBS gives the corresponding free alcohol R_(1′)=OH), followed by alkylation reaction of the hydroxyl group with a suitable alkylbromide or iodide in the presence of an appropriate base (e.g. potassium carbonate) in an organic solvent (e.g. tetrahydrofuran) at room or elevated temperature. In a final deprotection step the N-Boc protecting can be removed with an acid (e.g. HCl) in a suitable organic solvent (e.g. ethanol) to give compounds of formula I.

Indazole-3-carboxylates of general formula XI may be prepared from 3-unsubstituted indazole starting materials of formula XXI as depicted in Scheme 2. Iodination of starting materials XXI, for example, using N-iodosuccinimide in DMF at room temperature can be used to prepare 3-iodoindazoles of general formula XII. Methoxycarbonylation of intermediates XII under standard conditions using a carbonmonoxide in a pressure reactor in the presence of a palladium catalyst (e.g. Pd(dppf)Cl2) in methanol with triethylamine at an elevated temperature gives methyl indazole-3-carboxylates XIII.

In certain embodiments, X′ in the intermediates of formulas XI, XII, XIII and XV may bear a protecting group (e.g. THP) which is either removed concomitantly in the final Boc deprotection step, or may optionally be converted in separate additional deprotection and alkylation steps to the final X group. For example, preparation of N-substituted indazole isomer intermediate carboxaldehydes of general structure XIIIa and XIIIb is depicted in Scheme 3. Scheme 3 uses a THP protected intermediate with R₁ as an alkoxy group. Deprotection of the THP group then gives an intermediate which can be treated with a base and an alkylating agent R₂I to give a mixture of indazole nitrogen alkylated isomers XIIIa and XIIIb, typically favoring isomer XIIIa. After chromatographic separation, the individual isomers XXXIa and XIIIb can be converted as described in Scheme 1 to the corresponding N-alkyl indazole isomer compounds captured in Formula (I).

Examples

In order that the invention described herein may be more fully understood, the following examples are set forth. It should be understood that these examples are for illustrative purposes only and are not to be construed as limiting this invention in any manner.

Synthetic Methods

General methods and experimental procedures for preparing and characterizing compounds of the present invention are set forth below. Wherever needed, reactions were heated using conventional hotplate apparatus or heating mantle or microwave irradiation equipment. Reactions were conducted with or without stirring, under atmospheric or elevated pressure in either open or closed vessels. Reaction progress was monitored using conventional techniques such as TLC, HPLC, UPLC, or LCMS using instrumentation and methods described below. Reactions were quenched and crude compounds isolated using conventional methods as described in the specific examples provided. Solvent removal was carried out with or without heating, under atmospheric or reduced pressure, using either a rotary or centrifugal evaporator.

Compound purification was carried out as needed using a variety of traditional methods including, but not limited to, preparative chromatography under acidic, neutral, or basic conditions using either normal phase or reverse phase HPLC or flash columns or Prep-TLC plates. Compound purity and mass confirmations were conducted using standard HPLC and/or UPLC and/or MS spectrometers and/or LCMS and/or GC equipment (e.g., including, but not limited to the following instrumentation: Waters Alliance 2695 with 2996 PDA detector connected with ZQ detector and ESI source; Shimadzu LDMS-2020; Waters Acquity H Class with PDA detector connected with SQ detector and ESI source; Agilent 1100 Series with PDA detector; Waters Alliance 2695 with 2998 PDA detector; AB SCIEX API 2000 with ESI source; Agilent 7890 GC). Exemplified compounds were dissolved in either MeOH or MeCN to a concentration of approximately 1 mg/mL and analyzed by injection of 0.5-10 μL into an appropriate LCMS system using the methods provided in the following table:

Mobile Mobile Flow Rate MS Heat Temp Detector Voltage Method Column Phase A Phase B (mL/min) Gradient Profile (° C.) (kV) A Shim-pack Water/0.05% ACN/0.05% 1 5% to 100% B in 2.0 250 1.5 XR-ODS TFA TFA minutes, 100% B for 2.2 μm 1.1 minutes, 100% to 3.0 × 50 mm 5% B in 0.2 minutes, then stop B Gemini-NX Water/0.04% ACN 1 5% to 100% B in 2.0 200 0.75 3 μm C18 Ammonia minutes, 100% B for 110A 1.1 minutes, 100% to 5% B in 0.1 minutes, then stop C Shim-pack Water/0.05% ACN/0.05% 1 5% to 100% B in 2.0 250 0.85 XR-ODS FA FA minutes, 100% B for 1.6 μm 1.1 minutes, 100% to 2.0 × 50 mm 5% B in 0.1 minutes, then stop D Shim-pack Water/0.05% ACN/0.05% 1 5% to 100% B in 2.0 250 0.95 XR-ODS TFA TFA minutes, 100% B for 2.2 μm 1.1 minutes, 100% to 33.0 × 50 mm 5% B in 0.1 minutes, then stop E Waters Water/0.05% ACN/0.05% 0.9 5% to 100% B in 2.0 250 1.5 Xselect C18 FA FA minutes, 100% B for 3.5 μm 1.2 minutes, 100% to 33.0 × 50 mm 5% B in 0.1 minutes then stop F Shim-pack Water/0.05% ACN/0.05% 1 5% to 80% B in 3.25 200 0.95 XR-ODS TFA TFA minutes, 80% B for 2.2 μm 1.35 minutes, 80% to 33.0 × 50 mm 5% B in 0.1 minutes, then stop G Shim-pack Water/0.05% ACN/0.05% 1 5% to 70% B in 2.50 200 0.95 XR-ODS TFA TFA minutes, 70% B for 2.2 μm 0.70 minutes, 70% to 33.0 × 50 mm 5% B in 0.3 minutes, then stop H Shim-pack Water/0.05% ACN/0.05% 1 5% to 100% B in 2.20 250 0.95 XR-ODS TFA TFA minutes, 100% B for 2.2 μm 1.00 minutes, 100% to 33.0 × 50 mm 5% B in 0.1 minutes, then stop I Shim-pack Water/0.05% ACN/0.05% 1 5% to 100% B in 1.20 250 0.95 XR-ODS TFA TFA minutes, 100% B for 2.2 μm 1.00 minutes, 100% to 33.0 × 50 mm 5% B in 0.1 minutes, then stop J Shim-pack Water/0.05% ACN/0.05% 1 5% to 70% B in 3.20 250 0.95 XR-ODS TFA TFA minutes, 70% B for 2.2 μm 0.75 minutes, 70% to 33.0 × 50 mm 5% B in 0.35 minutes, then stop K Shim-pack Water/0.05% ACN/0.05% 1 5% to 80% B in 3.00 250 1.5 XR-ODS TFA TFA minutes, 80% B for 0.8 2.2 μm minutes, 80% to 5% B 33.0 × 50 mm in 0.1 minutes, then stop L Shim-pack Water/0.05% ACN/0.05% 1 5% to 100% B in 3.00 250 1.5 XR-ODS TFA TFA minutes, 100% B for 2.2 μm 0.8 minutes, 100% to 33.0 × 50 mm 5% B in 0.1 minutes, then stop M Shim-pack Water/0.05% ACN/0.05% 1 5% to 100% B in 2.20 250 1.5 XR-ODS TFA TFA minutes, 100% B for 2.2 μm 1.00 minutes, 100% to 33.0 × 50 mm 5% B in 0.1 minutes, then stop N Shim-pack Water/0.05% ACN/0.05% 1 5% to 80% B in 2.20 250 1.5 XR-ODS TFA TFA minutes, 80% B for 1.0 2.2 μm minutes, 80% to 5% B 33.0 × 50 mm in 0.1 minutes, then stop O Zorbax Water/0.05% ACN/0.05% 1 5% to 70% B in 8.00 250 1.5 Eclipse Plus TFA TFA minutes, 70% B for 2.0 C18 minutes, then stop 4.6 × 100 mm P Shim-pack Water/0.05% ACN/0.05% 1 5% to 65% B in 3.00 250 1.5 XR-ODS TFA TFA minutes, 65% B for 2.2 μm 0.80 minutes, 100% to 33.0 × 50 mm 5% B in 0.1 minutes, then stop Q Shim-pack Water/0.05% ACN/0.05% 1 5% to 60% B in 2.50 250 0.95 XR-ODS TFA TFA minutes, 60% B for 0.7 2.2 μm minutes, 60% to 5% B 33.0 × 50 mm in 0.1 minutes, then stop R Shim-pack Water/0.05% ACN/0.05% 1 5% to 50% B in 2.50 250 0.95 XR-ODS TFA TFA minutes, 50% B for 0.7 2.2 μm minutes, 50% to 5% B 33.0 × 50 mm in 0.1 minutes, then stop S XBridge Water/0.05% ACN/0.05% 1 5% to 95% B in 2.20 250 0.9 C18 3.5 μm TFA TFA minutes, 95% B for 33.0 × 50 mm 1.00 minutes, 95% to 5% B in 0.1 minutes, then stop T Shim-pack Water/0.05% ACN/0.05% 0.7 5% to 100% B in 2.0 250 0.85 XR-ODS FA FA minutes, 100% B for 1.6 μm 1.1 minutes, 100% to 2.0 × 50 mm 5% B in 0.1 minutes, then stop U Shim-pack Water/0.05% ACN/0.05% 1 5% to 40% B in 2.50 250 0.95 XR-ODS TFA TFA minutes, 40% B for 0.7 2.2 μm minutes, 40% to 5% B 33.0 × 50 mm in 0.1 minutes, then stop V Shim-pack Water/0.05% ACN/0.05% 1 5% to 60% B in 4.20 200 1.05 XR-ODS TFA TFA minutes, 60% B for 1.0 2.2 μm minutes, 60% to 5% B 33.0 × 50 mm in 0.1 minutes, then stop W Shim-pack Water/0.05% ACN/0.05% 1 5% to 100% B in 2.20 200 0.95 XR-ODS TFA TFA minutes, 100% B for 2. 2 μm 1.00 minutes, 100% to 33.0 × 50 mm 5% B in 0.1 minutes, then stop X Shim-pack Water/0.05% ACN/0.05% 0.7 5% to 100% B in 2.0 200 0.85 XR-ODS FA FA minutes, 100% B for 1.6 μm 1.1 minutes, 100% to 2.0 × 50 mm 5% B in 0.1 minutes, then stop Y Ecliplis Plus Water/0.05% ACN 1 5% to 100% B in 2.0 250 1 C18 3.5 μm TFA minutes, 100% B for 4.6 × 50 mm 1.0 minutes, 100% to 5% B in 0.1 minutes, then stop Z Ecliplis Plus Water/10 mM ACN/5% 1 5% to 100% B in 2.0 250 1.1 C18 3.5 μm ammonium water minutes, 100% B for 4.6 × 50 mm carbonate 1.0 minutes, 100% to 5% B in 0.1 minutes, then stop A1 Shim-pack Water/0.05% ACN 1 5% to 100% B in 2.0 250 1 XR-ODS TFA minutes, 100% B for 2.2 μm 1.0 minutes, 100% to 33.0 × 50 mm 5% B in 0.1 minutes, then stop A2 Ecliplis Plus Water/10 mM ACN 1 5% to 100% B in 2.0 250 0.95 C18 3.5 μm ammonium minutes, 100% B for 4.6 × 50 mm acetate 1.4 minutes, 100% to 5% B in 0.1 minutes, then stop A3 Acquity Water/5 mM ACN/0.1% 0.55 5% B at 0.01 min up to BEH C18 ammonium FA 0.4 min, 35% B at 0.8 1.7 μm acetate/0.1% min, 55% B at 1.2 min, 2.1 × 50 mm FA 100% B in 1.3 minutes, at 2.5 min up to 3.30 min, 5% B at 3.31 min up to 4.0 min, then stop A4 Shim-pack Water/0.05% ACN/0.05% 1 5% to 30% B in 8.0 250 1.5 XR-ODS TFA TFA minutes, 30% B for 2.0 33.0 × 50 mm minutes, then stop A5 Shim-pack Water/0.05% ACN/0.05% 1 5% to 100% B in 2.2 250 1.5 XR-ODS TFA TFA minutes, 100% B for 33.0 × 50 mm 1.0 minutes, 100% to 5% B in 0.1 minutes, then stop A6 Atlantis Water/0.05% ACN/0.05% 95% to 60% B in 4.0 250 1.5 HILIC TFA TFA minutes, 60% B for 4.0 3.0 × 100 mm 0.8 minutes, then stop A7 Shim-pack Water/0.05% ACN/0.05% 1 5% B for 0.5 minutes, 250 1.5 XR-ODS TFA TFA 5% to 75% B at 2.2 33.0 × 50 mm minutes, 100% B for 1.0 minutes, 100% to 5% B in 0.1 minutes, then stop A8 Zorbax SB- Water/0.05% ACN/0.05% 1.2 5% to 70% B in 10.0 250 1.05 C18 TFA TFA minutes, 70% B for 5.0 5 μm minutes, then stop 4.6 × 150 mm A9 Shim-pack Water/0.05% ACN/0.05% 1 5% to 40% B in 4.4 250 0.95 XR-ODS TFA TFA minutes, 40% B for 0.9 33.0 × 50 mm minutes, then stop A10 Atlantis T3 Water/0.05% ACN/0.05% 1 5% to 50% B in 8.0 200 1.05 3 μm TFA TFA minutes, 50% B for 2.0 4.6 × 100 mm minutes, then stop A11 Shim-pack Water/0.05% ACN/0.05% 1 5% B for 0.5 minutes, 250 1.50 XR-ODS TFA TFA 5% to 100% B in 1.7 33.0 × 50 mm minutes, 100% B for 1.0 minute, 100% to 5% B in 0.1 minute, then stop

Compound structure confirmations were carried out using standard 300 or 400 MHz NMR spectrometers with NOe's conducted whenever necessary.

The following abbreviations are used herein:

Abbreviation Meaning ACN acetonitrile atm. atmosphere DCM dichloromethane DHP dihydropyran DIBAL diisobutyl aluminum hydride DIEA diisopropyl ethylamine DMF dimethyl formamide DMF-DMA dimethyl formamide dimethyl acetal DMSO dimethyl sulfoxide dppf 1,1′-bis(diphenylphosphino)ferrocene EA ethyl acetate ESI electrospray ionization EtOH ethanol FA formic acid GC gas chromatography h hour Hex hexanes HMDS hexamethyl disilazide HPLC high performance liquid chromatography IPA isopropanol LCMS liquid chromatography/mass spectrometry MeOH methanol min minutes NBS N-bromo succinimide NCS N-chloro succinimide NIS N-iodo succinimide NMR nuclear magnetic resonance NOe nuclear Overhauser effect Prep. preparative PTSA para-toluene sulfonic acid Rf retardation factor rt room temperature RT retention time sat. saturated SGC silica gel chromatography TBAF tetrabutyl ammonium fluoride TEA triethylamine TFA trifluoroacetic acid THF tetrahydrofuran TLC thin layer chromatography UPLC ultra performance liquid chromatography

Compound 2 N1-((5-iso-butoxy-1H-indazol-3-yl)methyl)-N1-methylethane-1,2-diamine

Step 1: 5-(tert-butyldimethylsilyloxy)-1H-indazole

A solution of 1H-indazol-5-ol (25 g, 186.38 mmol, 1.00 equiv), imidazole (31.7 g, 466.18 mmol, 2.50 equiv) and tert-butyl(chloro)dimethylsilane (33.8 g, 224.25 mmol, 1.20 equiv) in N,N-dimethylformamide (100 mL) was stirred at room temperature for 2 h. The reaction was quenched by the addition of water/ice (200 mL). The precipitate was collected by filtration and dried in a vacuum oven to give 45 g (97%) of 5-(tert-butyldimethylsilyloxy)-1H-indazole as a brown solid. ¹H-NMR (300 MHz, CDCl₃): δ 8.00 (s, 1H), 7.40 (d, J=9.0 Hz, 1H), 7.15 (d, J=9.0 Hz, 1H), 7.02 (dd, J=9.0 Hz, 2.4 Hz, 1H), 1.03 (s, 9H), 0.24 (s, 6H) ppm. LCMS (method D, ESI): RT=1.66 min, m/z=249.0 [M+H]⁺.

Step 2: 5-(tert-butyldimethylsilyloxy)-3-iodo-1H-indazole

To a solution of 5-[(tert-butyldimethylsilyl)oxy]-1H-indazole (13 g, 52.34 mmol, 1.00 equiv) in N,N-dimethylformamide (550 mL) maintained under nitrogen was added NIS (28.6 g, 104.76 mmol, 2.00 equiv) in portions. The reaction mixture was stirred at room temperature overnight and then concentrated under vacuum. The residue was purified on a silica gel column eluted with 0-10% of ethyl acetate in petroleum ether to give 19.2 g (98%) of 5-(tert-butyldimethylsilyloxy)-3-iodo-1H-indazole as an off-white solid. ¹H-NMR (300 MHz, CDCl₃): δ 7.50-7.45 (m, 1H), 7.09 (dd, J=9.0 Hz, 2.1 Hz, 1H), 6.98-6.70 (m, 1H), 1.10 (s, 9H), 0.24 (s, 6H) ppm. LCMS (method A, ESI): RT=1.80 min, m/z=374.9 [M+H]⁺.

Step 3: (R/S) 5-(tert-butyldimethylsilyloxy)-3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole

A solution of (R/S) 5-(tert-butyldimethylsilyloxy)-3-iodo-1H-indazole (9.6 g, 25.65 mmol, 1.00 equiv), 3,4-dihydro-2H-pyran (6.47 g, 77.02 mmol, 3.00 equiv) and p-toluenesulfonic acid (440 mg, 2.56 mmol, 0.10 equiv) in THF (100 mL) was stirred at room temperature for 3 h. The reaction mixture was diluted with 100 mL of H₂O and then extracted with 3×200 mL of dichloromethane. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 0-10% of ethyl acetate in petroleum ether to give 11 g (94%) of (R/S) 5-(tert-butyldimethylsilyloxy)-3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole as a light brown oil. LCMS (method D, ESI): RT=1.45 min, m/z=459.0 [M+H]⁺.

Step 4: (R/S) methyl 5-(tert-butyldimethylsilyloxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carboxylate

A mixture of (R/S) 5-(tert-butyldimethylsilyloxy)-3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole (5 g, 10.91 mmol, 1.00 equiv), Pd(dppf)Cl2 (800 mg, 1.09 mmol, 0.10 equiv) and triethylamine (3.3 g, 32.61 mmol, 2.99 equiv) in methanol (50 mL) was stirred under 10 atm. of carbon monoxide in a 100-mL pressure reactor at 60° C. for 5 h. The reaction was cooled to room temperature then concentrated under vacuum. The residue was diluted with 20 mL of H₂O and the resulting mixture was extracted with 3×50 mL of dichloromethane. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 0-7% of ethyl acetate in petroleum ether to yield 2.6 g (61%) of (R/S) methyl 5-(tert-butyldimethylsilyloxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carboxylate as a colorless oil. ¹H-NMR (300 MHz, CDCl₃): δ 7.62-7.57 (m, 2H), 7.04 (dd, J=9.0 Hz, 2.4 Hz, 1H), 5.82-5.78 (m, 1H), 3.85-3.70 (m, 2H), 3.68-3.47 (m, 1H), 2.63-2.45 (m, 1H), 2.10 (s, 3H), 1.08-1.05 (m, 4H), 1.05 (s, 9H), 0.25 (s, 6H) ppm. LCMS (method E, ESI): RT=1.90 min, m/z=391.1 [M+H]⁺.

Step 5: (R/S) (5-(tert-butyldimethylsilyloxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methanol

To a stirred mixture of LiAH₄ (390 mg, 11.50 mmol, 1.00 equiv) in anhydrous THF (100 mL) maintained under nitrogen at −70° C. was added dropwise a solution of (R/S) methyl 5-(tert-butyldimethylsilyloxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carboxylate (1.33 g, 3.41 mmol, 1.00 equiv) in THF. The reaction was stirred at −40° C. for 1 h and then quenched by the addition of 20 mL of saturated NH₄Cl solution. The resulting mixture was concentrated under vacuum to remove the excess THF. The mixture was extracted with 3×50 mL of dichloromethane. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 0-20% of ethyl acetate in petroleum ether to afford 1 g (81%) of (R/S) (5-(tert-butyldimethylsilyloxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methanol as a white solid. ¹H-NMR (300 MHz, CDCl₃): δ 7.22 (d, J=9.0 Hz, 1H), 6.95 (d, J=2.1 Hz, 1H), 6.80 (dd, J=8.7 Hz, 2.1 Hz, 1H), 5.44-5.40 (m, 1H), 4.80 (s, 2H), 3.80-3.71 (m, 2H), 2.01-1.75 (m, 2H), 1.69-1.25 (m, 4H), 0.80 (s, 9H), 0.10 (s, 6H) ppm. LCMS (method A, ESI): RT=1.71 min, m/z=363.0 [M+H]⁺.

Step 6: (R/S) 5-(tert-butyldimethylsilyloxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde

A mixture of (R/S) (5-(tert-butyldimethylsilyloxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methanol (1 g, 2.76 mmol, 1.00 equiv) and MnO₂ (2.4 g, 27.61 mmol, 10.01 equiv) in dichloromethane (10 mL) was stirred at room temperature for 5 h. The solid material was removed by filtration. The filtrate was concentrated under vacuum to give 0.8 g (80%) of 5-(tert-butyldimethylsilyloxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde as a colorless oil. ¹H-NMR (400 MHz, CDCl₃): δ 10.0 (s, 1H), 7.44 (s, 1H), 7.29 (d, J=8.8 Hz, 1H), 6.81 (d, J=1.2 Hz, 1H), 5.57-5.54 (m, 1H), 3.85-3.70 (m, 2H), 3.42-3.20 (m, 2H), 1.70-1.35 (m, 4H), 0.80 (s, 9H), 0.10 (s, 6H) ppm. LCMS (method A, ESI): RT=1.88 min, m/z=360.9 [M+H]⁺.

Step 7: (R/S) 5-hydroxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde

A solution of (R/S) 5-(tert-butyldimethylsilyloxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde (150 mg, 0.42 mmol, 1.00 equiv) and TBAF (800 mg, 800.00 mmol, 1922.79 equiv) in THF (5 mL) was stirred at room temperature for 2 h. The reaction mixture was diluted with 10 mL of H₂O and then extracted with 3×20 mL of dichloromethane. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 10-20% of ethyl acetate in petroleum ether to give 0.1 g (98%) of (R/S) 5-hydroxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde as an off-white solid. LCMS (method A, ESI): RT=1.33 min, m/z=246.0 [M+H].

Step 8: 5-iso-butoxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde

A mixture of (R/S) 5-hydroxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde (200 mg, 0.81 mmol, 1.00 equiv), 1-iodo-2-methylpropane (300 mg, 1.63 mmol, 2.01 equiv) and Cs₂CO₃ (270 mg, 0.83 mmol, 1.02 equiv) in N,N-dimethylformamide (10 mL) was stirred under nitrogen at 70° C. for 5 h. The resulting solution was cooled to room temperature and diluted with 10 mL of H₂O. The mixture was extracted with 3×20 mL of ethyl acetate. The combined organic layers were washed with 3×20 mL of brine, dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 0-15% of ethyl acetate in petroleum ether to give 0.165 g (67%) of (R/S) 5-iso-butoxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde as a white solid. ¹H-NMR (300 MHz, DMSO-d6): δ 10.16 (s, 1H), 7.83 (d, J=9.3 Hz, 1H), 7.51 (d, J=2.1 Hz, 1H), 7.22 (dd, J=9.3 Hz, 2.4 Hz, 1H), 6.04-6.01 (m, 1H), 4.07-4.00 (m, 1H), 3.92-3.75 (m, 4H), 2.12-2.00 (m, 2H), 1.63-1.62 (m, 2H), 1.24-1.16 (m, 2H), 1.04 (d, J=6.6 Hz, 6H) ppm. LCMS (method A, ESI): RT=1.71 min, m/z=218.9 [M+H-THP]⁺.

Step 9: (R/S) tert-butyl 2-(((5-iso-butoxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)carbamate

To a solution of (R/S) 5-(2-methylpropoxy)-1-(oxan-2-yl)-1H-indazole-3-carbaldehyde (200 mg, 0.66 mmol, 1.00 equiv) and tert-butyl N-[2-(methylamino)ethyl]carbamate (140 mg, 0.80 mmol, 1.21 equiv) in 1,2-dichloroethane (10 mL) was added NaBH(AcO)₃ (420 mg, 1.98 mmol, 3.00 equiv). The resulting solution was stirred at room temperature for 3 h and then diluted with 10 mL of H₂O. The mixture was extracted with 3×20 mL of dichloromethane. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 10-50% of ethyl acetate in petroleum ether to give 0.15 g (49%) of (R/S) tert-butyl 2-(((5-iso-butoxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)carbamate as a colorless oil. ¹H-NMR (300 MHz, CDCl₃): δ 7.55-7.40 (m, 1H), 7.21-7.00 (m, 2H), 5.75-5.50 (m, 1H), 5.30 (s, 2H), 4.20-3.85 (m, 2H), 3.85-3.55 (m, 2H), 3.50-3.10 (m, 2H), 2.05 (s, 3H), 1.97-1.60 (m, 4H), 1.44 (s, 9H), 1.38-1.19 (m, 5H), 1.05 (d, J=6.6 Hz, 6H) ppm. LCMS (method A, ESI): RT=3.37 min, m/z=461.1 [M+H]⁺.

Step 10: N¹-((5-iso-butoxy-1H-indazol-3-yl)methyl)-N′-methylethane-1,2-diamine (Compound 2)

A solution of (R/S) tert-butyl 2-(((5-iso-butoxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)carbamate (150 mg, 0.33 mmol, 1.00 equiv) in 3N hydrochloric acid (10 mL) was stirred at 60° C. for 3 h. The resulting mixture was concentrated under vacuum and the crude product was purified by Prep-HPLC with the following conditions (Waters-1): Column, XBridge Shield RP 18, 5 μm, 19×150 mm; mobile phase, phase A: water with 0.2% TFA; phase B: CH₃CN (10% CH₃CN up to 43% in 10 min, up to 100% in 13 min; Detector, UV 254 nm to give 67.9 mg (41%) of N¹-((5-iso-butoxy-1H-indazol-3-yl)methyl)-N¹-methylethane-1,2-diamine trifluoroacetate as a light brown solid. ¹H-NMR (300 MHz, D₂O): δ 7.57 (d, J=9.0 Hz, 1H), 7.24-7.17 (m, 2H), 4.74-4.71 (m, 2H), 3.84 (d, J=6.6 Hz, 2H), 3.58-3.42 (m, 4H), 2.92 (s, 3H), 2.07-1.98 (m, 1H), 0.96 (d, J=6.6 Hz, 6H) ppm. LCMS (method X, ESI): RT=0.82 min, m/z=277.1 [M+H]⁺.

Compound 3 N¹-((5-iso-butoxy-1-methyl-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine

Step 1: (R/S) 5-iso-butoxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde

A mixture of (R/S) 5-hydroxy-1-(oxan-2-yl)-1H-indazole-3-carbaldehyde (590 mg, 2.40 mmol, 1.00 equiv), 1-iodo-2-methylpropane (882.6 mg, 4.80 mmol, 2.00 equiv) and cesium carbonate (782 mg, 2.39 mmol, 1.00 equiv) and N,N-dimethylformamide (15 mL) was stirred under nitrogen overnight at 60° C. The reaction was cooled to room temperature then quenched by the addition of 50 mL of water/ice. The resulting mixture was extracted with 3×50 mL of ethyl acetate. The combined organic layers was washed with 3×50 mL of brine, dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 15-35% of ethyl acetate in petroleum ether to give 250 mg (35%) of (R/S) 5-iso-butoxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde as a yellow solid. ¹H-NMR (300 MHz, CDCL₃): δ 10.25 (s, 1H), 7.65 (d, J=2.1 Hz, 1H), 7.59 (d, J=9.0 Hz, 1H), 7.16 (dd, J=9.0 Hz, 2.1 Hz, 1H), 5.83 (d, J=6.9 Hz, 1H), 4.05 (m, 1H), 3.83 (d, J=6.6 Hz, 2H), 3.80 (m, 1H), 2.60 (m, 1H), 2.15 (m, 3H), 1.80 (m, 3H), 1.08 (d, J=6.9 Hz, 6H) ppm. LCMS (method D, ESI): RT=1.77 min, m/z=303.1 [M+H]⁺.

Step 2: 5-iso-butoxy-1H-indazole-3-carbaldehyde

A solution of 5-iso-butoxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde (250 mg, 0.83 mmol, 1.00 equiv) in 12N hydrochloric acid (3 mL), ethanol (3 mL) and 1,4-dioxane (6 mL) was stirred overnight at room temperature. The reaction mixture was concentrated under vacuum and the pH value of the solution was adjusted to 8 with saturated sodium bicarbonate solution. The resulting mixture was extracted with 3×50 mL of dichloromethane. The organic layers were combined, dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 60-100% of ethyl acetate in petroleum ether to yield 110 mg (61%) of 5-iso-butoxy-1H-indazole-3-carbaldehyde as a yellow solid. ¹H-NMR (300 MHz, DMSO-d₆): δ 10.16 (s, 1H), 7.61 (d, J=9.0 Hz, 1H), 7.48 (d, J=2.1 Hz, 1H), 7.14 (dd, J=9.0 Hz, 2.1 Hz, 1H), 3.80 (d, J=6.6 Hz, 1H), 2.10-2.05 (m, 1H), 1.01 (d, J=6.6 Hz, 6H) ppm. LCMS (method D, ESI): RT=1.50 min, m/z=219.1 [M+H]⁺.

Step 3: 5-iso-butoxy-1-methyl-1H-indazole-3-carbaldehyde

A mixture of 5-iso-butoxy-1H-indazole-3-carbaldehyde (110 mg, 0.50 mmol, 1.00 equiv), potassium carbonate (209 mg, 1.50 mmol, 2.98 equiv) and methyl iodide (107.5 mg, 0.76 mmol, 1.50 equiv) in acetonitrile (4 mL) was stirred at room temperature overnight. The resulting mixture was concentrated under vacuum and the residue was filtered through a silica gel column eluted with 2-5% of ethyl acetate in petroleum ether. The crude product (70 mg) was purified by Pre-HPLC with the following conditions (1#-Pre-HPLC-005(Waters)): Column, XBridge Shield RP18 OBD Column, 5 μm, 19×50 mm; mobile phase, water with 10 mmol NH₄HCO₃ and CH₃CN (18% CH₃CN up to 58% in 10 min, up to 95% in 1 min, down to 18% in 2 min); Detector, UV 254/220 nm to give 35 mg (30%) of 5-iso-butoxy-1-methyl-1H-indazole-3-carbaldehyde as a white solid. ¹H-NMR (400 MHz, CDCl₃): δ 10.1 (s, 1H), 7.55 (d, J=2.0 Hz, 1H), 7.27 (d, J=8.8 Hz, 1H), 7.07 (dd, J=8.8 Hz, 2.0 Hz, 1H), 4.08 (s, 3H), 3.74 (d, J=6.8 Hz, 2H), 2.09-2.02 (m, 1H), 0.98 (d, J=6.8 Hz, 6H) ppm. LCMS (method D, ESI): RT=2.23 min, m/z=233.1 [M+H]+ and 15 mg (13%) of 5-iso-butoxy-2-methyl-2H-indazole-3-carbaldehyde as a white solid. ¹H-NMR (400 MHz, CDCl₃): 10.12 (s, 1H), 7.62 (d, J=9.2 Hz, 1H), 7.17 (d, J=2.4 Hz, 1H), 7.07 (dd, J=9.2 Hz, 2.4 Hz, 1H), 4.38 (s, 3H), 3.73 (d, J=6.4 Hz, 2H), 2.10-2.05 (m, 1H), 0.99 (d, J=6.8 Hz, 6H) ppm. LCMS (method D, ESI): RT=2.24 min, m/z=233.1[M+H]⁺.

Step 4: tert-butyl 2-(((5-iso-butoxy-1-methyl-1H-indazol-3-yl)methyl)(methyl)amino) ethyl)(methyl)carbamate

To a solution of 5-iso-butoxy-1-methyl-1H-indazole-3-carbaldehyde (35 mg, 0.15 mmol, 1.00 equiv) and tert-butyl N-methyl-N-[2-(methylamino)ethyl]carbamate (34 mg, 0.18 mmol, 1.20 equiv) in 1,2-dichloroethane (3 mL) was added NaBH(OAc)₃ (96 mg, 0.45 mmol, 3.01 equiv). The resulting solution was stirred at room temperature for 8 h then quenched with 20 mL of water/ice. The resulting mixture was extracted with 3×20 mL of dichloromethane. The organic layers were combined, dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 0-100% of ethyl acetate to give 48 mg (79%) of tert-butyl 2-(((5-iso-butoxy-1-methyl-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate as a colorless oil. LCMS (method C, ESI): RT=0.86 min, m/z=405.3 [M+H].

Step 5: N¹-((5-iso-butoxy-1-methyl-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine (Compound 3)

A solution of tert-butyl 2-(((5-iso-butoxy-1-methyl-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (48 mg, 0.12 mmol, 1.00 equiv) in 3N hydrochloric acid (10 mL) was stirred at 60° C. for 2 h. The resulting solution was washed with 3×50 mL of dichloromethane. The aqueous layer was concentrated under vacuum and the crude product was purified by Prep-HPLC with the following conditions (2#-Waters 2767-2(HPLC-08)): Column, XBridge Shield RP 18, 5 μm, 19×150 mm; mobile phase, water with 50 mmol CF₃COOH and CH₃CN (10.0% CH₃CN up to 28.0% in 2 min, up to 46.0% in 10 min, up to 100.0% in 1 min, down to 10.0% in 1 min); Detector, UV 254 nm to give 31.3 mg (50%) of N¹-((5-iso-butoxy-1-methyl-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine trifluoroacetate as a colorless oil. ¹H-NMR (300 MHz, D₂O): δ 7.53 (d, J=10.5 Hz, 1H), 7.23-7.21 (m, 2H), 4.68-4.65 (m, 2H), 4.02 (s, 3H), 3.83 (d, J=6.9 Hz, 2H), 3.63-3.44 (m, 4H), 2.89 (s, 3H), 2.72 (s, 3H), 2.10-1.93 (m, 1H), 0.94 (d, J=6.6 Hz, 6H) ppm. LCMS (method W, ESI): RT=1.31 min, m/z=305.1 [M+H]⁺.

Compound 5 N¹-((5-(2-methoxyethoxy)-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine

Step 1: (R/S) 5-(2-methoxyethoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde

A solution of 5-hydroxy-1-(oxan-2-yl)-1H-indazole-3-carbaldehyde (120 mg, 0.49 mmol, 1.00 equiv), Cs₂CO₃ (180 mg, 0.55 mmol, 2.00 equiv) and 1-bromo-2-methoxyethane (500 mg, 3.60 mmol, 3.00 equiv) in N,N-dimethylformamide (2 mL) was stirred at room temperature for 10 h. The reaction was diluted with 50 mL of ethyl acetate and then washed with 4×10 mL of brine. The organic layer was dried over anhydrous sodium sulfate then concentrated under vacuum to give 134 mg (90%) of (R/S) 5-(2-methoxyethoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde as a yellow oil. LCMS (method D, ESI): RT=1.48 min, m/z=305.1 [M+H]⁺.

Step 2: (R/S) tert-butyl 2-(((5-(2-methoxyethoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

To a solution of (R/S) 5-(2-methoxyethoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde (130 mg, 0.43 mmol, 1.00 equiv) and tert-butyl N-methyl-N-[2-(methylamino)ethyl]carbamate (180 mg, 0.96 mmol, 2.50 equiv) in 1,2-dichloroethane (3 mL) was added NaBH(OAc)₃ (260 mg, 1.23 mmol, 3.00 equiv). The resulting solution was stirred at room temperature for 2 h. The pH value of the solution was adjusted to 10 with 5% potassium carbonate solution. The resulting solution was extracted with 4×10 mL of dichloromethane. The combined organic layers was concentrated under vacuum to give 156 mg (77%) of (R/S) tert-butyl 2-(((5-(2-methoxyethoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate as a yellow oil. LCMS (method A, ESI): RT=1.32 min, m/z=477.2 [M+H]⁺.

Step 3: N¹-((5-(2-methoxyethoxy)-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine (Compound 5)

A solution of (R/S) tert-butyl N-[2-([[5-(2-methoxyethoxy)-1-(oxan-2-yl)-1H-indazol-3-yl]methyl](methyl)amino)ethyl]-N-methylcarbamate (156 mg, 0.33 mmol, 1.00 equiv) in trifluoroacetic acid (3 mL) and dichloromethane (2 mL) was stirred at room temperature for 4 h. The reaction mixture was concentrated under vacuum and the crude product was purified by Prep-HPLC with the following conditions: Column, XBridge Shield RP 18, 5 μm, 19×150 mm; mobile phase, water with 50 mmol CF₃COOH and CH₃CN (10.0% CH₃CN up to 28.0% in 2 min, up to 46.0% in 10 min, up to 100.0% in 1 min, down to 10.0% in 1 min); Detector, UV 254 nm to give 122.3 mg (70%) of N¹-((5-(2-methoxyethoxy)-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine trifluoroacetate as a colorless oil. ¹H-NMR (300 MHz, D₂O): δ 7.54 (d, J=9.0 Hz, 1H), 7.22 (d, J=1.8 Hz, 1H), 7.16 (dd, J=9.0 Hz, 2.1 Hz, 1H), 4.78-4.72 (m, 2H), 4.20-4.13 (m, 2H), 3.80-3.74 (m, 2H), 3.60-3.42 (m, 4H), 3.36 (s, 3H), 2.89 (s, 3H), 2.70 (s, 3H) ppm. LCMS (method M, ESI): RT=1.00 min, m/z=293.0 [M+H]⁺.

Compound 10 N¹,N²-dimethyl-N¹-((5-phenoxy-1H-indazol-3-yl)methyl)ethane-1,2-diamine

Step 1: (R/S) 5-(4-nitrophenoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde

A mixture of 1-fluoro-4-nitrobenzene (258 mg, 1.83 mmol, 1.00 equiv), (R/S) 5-hydroxy-1-(oxan-2-yl)-1H-indazole-3-carbaldehyde (300 mg, 1.22 mmol, 0.67 equiv) and Cs₂CO₃ (1.2 g, 3.68 mmol, 2.01 equiv) in 1,4-dioxane (25 mL) was stirred at 100° C. for 4 h. The reaction mixture was cooled to room temperature and then diluted with 50 mL of H₂O. The resulting mixture was extracted with 3×200 mL of ethyl acetate. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 0-13% of ethyl acetate in petroleum ether to give 350 mg (52%) of (R/S) 5-(4-nitrophenoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde as a light yellow solid. ¹H-NMR (300 MHz, CDCl₃): δ 10.3 (s, 1H), 8.23-8.18 (m, 2H), 8.01 (s, 1H), 7.78-7.75 (m, 1H), 7.27-7.23 (m, 1H), 7.04-7.00 (m, 1H), 5.89-5.85 (m, 1H), 4.06-4.01 (m, 1H), 3.85-3.77 (m, 1H), 2.60-2.52 (m, 1H), 2.21-2.17 (m, 2H), 1.86-1.74 (m, 3H) ppm.

Step 2: (R/S) tert-butyl methyl(2-(methyl((5-(4-nitrophenoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate

To a solution of (R/S) 5-(4-nitrophenoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde (300 mg, 0.82 mmol, 1.00 equiv) and tert-butyl N-methyl-N-[2-(methylamino)ethyl]carbamate (170 mg, 0.90 mmol, 1.11 equiv) in 1,2-dichloroethane (40 mL) was added NaBH(OAc)₃ (520 mg). The reaction was stirred at room temperature overnight and then quenched with 50 mL of water. The resulting mixture was extracted with 3×200 mL of ethyl acetate. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 0-10% of ethyl acetate in petroleum ether to give 420 mg (95%) of (R/S) tert-butyl methyl(2-(methyl((5-(4-nitrophenoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate as a colorless oil. ¹H-NMR (400 MHz, CDCl₃): δ 8.18 (m, 2H), 7.71-7.55 (m, 2H), 7.20-7.09 (m, 1H), 7.05-6.93 (m, 2H), 5.70-5.68 (m, 1H), 4.11-4.09 (m, 1H), 4.06-3.91 (m, 1H), 3.79-3.73 (m, 1H), 3.50-3.33 (m, 1H), 2.79 (s, 3H), 2.57-2.52 (m, 2H), 2.49-2.17 (m, 2H), 2.17-2.05 (m, 1H), 1.80-1.68 (m, 4H), 1.42 (s, 9H) ppm.

Step 3: (R/S) tert-butyl 2-(((5-(4-aminophenoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

A mixture of (R/S) tert-butyl methyl(2-(methyl((5-(4-nitrophenoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate (550 mg, 1.02 mmol, 1.00 equiv) and Raney/Ni (500 mg) in methanol (30 mL) was stirred under hydrogen at room temperature for 30 min. The catalyst was removed by filtration. The filtrate was concentrated under vacuum to give 400 mg (77%) of (R/S) tert-butyl 2-(((5-(4-aminophenoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl(methyl)carbamate as a colorless oil. ¹H-NMR (300 MHz, CDCl₃): δ 7.52-7.49 (m, 2H), 7.33-7.26 (m, 2H), 7.18-7.12 (m, 1H), 6.90-6.80 (m, 2H), 6.71-6.61 (m, 2H), 5.70-5.68 (m, 1H), 4.11-4.09 (m, 1H), 4.07-3.91 (m, 1H), 3.79-3.73 (m, 1H), 3.71-3.33 (m, 1H), 2.79 (s, 3H), 2.57-2.52 (m, 2H), 2.49-2.17 (m, 2H), 2.17-2.05 (m, 1H), 1.80-1.68 (m, 4H), 1.42 (s, 9H) ppm.

Step 4: (R/S) tert-butyl methyl(2-(methyl((5-phenoxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate

To a stirred solution of (R/S) tert-butyl 2-(((5-(4-aminophenoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (400 mg, 0.78 mmol, 1.00 equiv) in hypophosphorous acid (10 mL) at 0° C. was added dropwise a solution of sodium nitrite (135 mg, 1.96 mmol, 2.49 equiv) in water (5 mL). The reaction was stirred at 0° C. for 30 min then the pH value of the solution was adjusted to 8 with saturated sodium carbonate solution. The resulting mixture was extracted with 3×200 mL of ethyl acetate. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 0-12.5% of ethyl acetate in petroleum ether to give 300 mg (77%) of (R/S) tert-butyl methyl(2-(methyl((5-phenoxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate as a colorless oil. LCMS (method A, ESI): RT=1.40 min, m/z=495.2 [M+H]⁺.

Step 5: N¹,N²-dimethyl-N¹-((5-phenoxy-1H-indazol-3-yl)methyl)ethane-1,2-diamine (Compound 10)

A solution of (R/S) tert-butyl methyl(2-(methyl((5-phenoxy-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate (250 mg, 0.51 mmol, 1.00 equiv) in 3N hydrochloric acid (20 mL) was stirred at room temperature overnight. The reaction was concentrated under vacuum and the residue was purified by Pre-HPLC with the following conditions (1#-Pre-HPLC-005 (Waters)): Column, SunFire Prep C18 OBD Column, 5 μm, 19×150 mm; mobile phase, phase A: water with 0.05% TFA. Phase B: MeCN (5% CH₃CN up to 17% in 10 min, down to 0% in 0 min); Detector, UV 254/220 nm to afford 62.3 mg (23%) of N¹,N²-dimethyl-N¹-((5-phenoxy-1H-indazol-3-yl)methyl)ethane-1,2-diamine trifluoroacetate as a white oil. ¹H-NMR (300 MHz, D₂O): δ 7.68 (d, J=9.0 Hz, 1H), 7.42-7.35 (m, 3H), 7.32-7.25 (m, 1H), 7.15 (t, J=7.2 Hz, 1H), 7.02 (d, J=7.8 Hz, 2H), 4.70 (s, 2H), 3.60-3.43 (m, 4H), 2.88 (s, 3H), 2.71 (s, 3H) ppm. LCMS (method M, ESI): RT=1.25 min, m/z=311.1 [M+H]⁺.

Compound 25 N¹,N²-dimethyl-N¹-((5-((tetrahydrofuran-3-yl)oxy)-1H-indazol-3-yl)methyl)ethane-1,2-diamine

Step 1: tert-butyl methyl(2-(methyl((5-((tetrahydrofuran-3-yl)oxy)-1-tosyl-1H-indazol-3-yl)methyl)amino)ethyl)carbamate

A solution of tert-butyl (2-(((5-hydroxy-1-tosyl-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (0.15 g, 0.0003 mole), tetrahydrofuran-3-ol (0.033 g, 0.00033 mole), 50% tributyl phosphine (0.09 g, 0.00046 mole) and 1,1 diazocarbonyl dipiperazine (0.1 g, 0.00046 mole) in toluene (2 ml) was stirred at room temperature for 4 hrs. The reaction mixture was poured into cold water and extracted with ethyl acetate (50 ml×2). The combined organic extracts were dried over sodium sulphate and distilled under reduced pressure to get the crude material. The crude product was purified by Combi flash and product eluted in 40% ethyl acetate in hexane to obtained the pure compound (0.1 g, Yield: 43.85%).

Step 2: tert-butylmethyl(2-(methyl((5-((tetrahydrofuran-3-yl)oxy)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate

A solution of tert-butyl methyl(2-(methyl((5-((tetrahydrofuran-3-yl)oxy)-1-tosyl-1H-indazol-3-yl)methyl)amino)ethyl)carbamate (0.1 g, 0.00017 mole) and sodium hydroxide (0.035 g, 0.0008 mole) in MeOH (1 ml) was heated to 50° C. for 1 hr. The reaction mixture was diluted with water, the product extracted in ethyl acetate, and the separated organic layer dried over sodium sulphate and distilled under reduced pressure to get 0.07 g of crude title compound.

Step 3: N¹,N²-dimethyl-N¹-((5-((tetrahydrofuran-3-yl)oxy)-1H-indazol-3-yl)methyl) ethane-1,2-diamine (Compound 25)

A solution of tert-butyl methyl(2-(methyl((5-((tetrahydrofuran-3-yl)oxy)-1H-indazol-3-yl)methyl)amino)ethyl) carbamate (0.07 g) and TFA (1 ml) in DCM (2 ml) was stirred 70° C. for 1 h. The reaction mixture was concentrated to get the crude material. The crude product was purified by prep. HPLC to get the pure product as the TFA salt (0.015 g, Yield: 46.15%). LCMS: 99.52% (m/z): 305.3 [M+1]⁺, HPLC: 99.68% ¹H-NMR (400 MHz, MeOD): δ 7.52 (d, 1H, J=9.2 Hz), 7.28 (s, 1H), 7.12 (d, 1H, J=2.4 Hz), 5.51 (s, 1H), 5.1-5.12 (q, 1H), 4.66 (s, 2H), 3.99-4.04 (m, 3H), 3.89-3.97 (m, 1H), 3.46-3.5 (m, 4H), 2.89 (s, 3H), 2.28-2.34 (m, 2H), 2.16-2.2 (m, 2H) ppm.

Compound 27 N¹-((5-(3-chlorophenoxy)-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine

Step 1: N-methoxy-N-methyl-1H-indazole-3-carboxamide

To a stirred solution of 1H-indazole-3-carboxylic acid (23 g, 141 mmol) in THF (1400 ml) was added N,O-dimethylhydroxylamine.HCl (16.5 g, 169.2 mmol) followed by dry pyridine (13.6 ml, 169.2 mmol) at 0° C. The reaction mixture was allowed to stir at room temperature for 2 hrs followed by addition of EDC.HCl (32.8 g, 211.5 mmol) and dry pyridine (28.5 ml, 352.5 mmol). The reaction mixture was allowed to stir overnight at room temperature. The reaction mixture was concentrated to dryness and 1500 ml of water was added to it. The resulting mixture was allowed to stir at RT for 30 mins. The precipitates were filtered and washed with diethyl ether to get pure product as yellow solid. (22 g, yield: 75.6%).

Step 2: 5-iodo-N-methoxy-N-methyl-1H-indazole-3-carboxamide

To a solution of N-methoxy-N-methyl-1H-indazole-3-carboxamide (10.2 g 49.7 mmol) in 180 ml of DCM was added bis(trifluoroacetoxy)iodobenzene (23.4 g, 54.67 mmol) at room temperature and stirred for 5 min, then a solution of iodine (7.6 g, 29.82 mmol) in DCM (400 ml) was added dropwise over a period of 0.5 h and stirred for 8 h. The reaction progress was monitored by TLC. After completion of the reaction, it was diluted with saturated solution of sodium thiosulphate and extracted with DCM (3×150 ml). The combined organic extracts were dried over sodium sulphate and distilled under reduced pressure to get crude material. The crude product was purified by trituration with hexane to obtain the title compound (12.2 g, Yield: 74.13%). ¹H-NMR (400 MHz, DMSO-d6): δ 13.81 (s, 1H), 8.40 (s, 1H), 7.66-7.67 (d, J=1.6 Hz, 1H), 7.49-7.51 (d, J=8.8 Hz, 1H), 3.78 (s, 3H), 3.45 (s, 3H) ppm. LCMS: 68.17% (m/z): 331.91[M+H]+.

Step 3: 5-iodo-N-methoxy-N-methyl-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carboxamide

To a solution of 5-iodo-N-methoxy-N-methyl-1H-indazole-3-carboxamide (1.0 g, 3.02 mmol) in 30 ml of DCM was added PTSA (0.575 g, 3.02 mmol) and stirred vigorously for 10 min at RT. Then 3,4-dihydro-2H-pyran (0.635 g, 7.55 mmol) was added dropwise and stirred for another 2 h. The reaction progress was monitored by TLC. After completion of the reaction, it was diluted with water and extracted with DCM (3×50 ml). The combined organic extracts were dried over sodium sulphate and distilled under reduced pressure to get crude material. The residue was purified by column chromatography using 3-4% MeOH: DCM as eluent to obtain the title compound (1.0 g, Yield: 80%). LCMS: 83.73% (m/z): 416.14[M+H]+.

Step 4: 5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde

To a solution of 5-iodo-N-methoxy-N-methyl-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carboxamide (0.5 g, 1.2 mmol) in 5 ml of dry THF at −50° C. under argon atmosphere was added dropwise 1M LAH in THF (0.3 mmol) and stirred for 1 h at −50° C. The reaction progress was monitored by TLC. After completion of the reaction, it was poured into saturated ammonium chloride solution and extracted with ethyl acetate (3×25 ml). The combined organic extracts were dried over sodium sulphate and distilled under reduced pressure to give title compound (0.4 g, Yield: 93%). ¹H-NMR (400 MHz, DMSO-d6): δ 10.17 (s, 1H), 8.50 (s, 1H), 7.78-7.86 (m, 2H), 6.07 (dd, J=9.2 Hz, 2.0 1H), 3.78-3.91 (m, 2H), 2.38-2.40 (m, 1H), 2.05-2.08 (m, 2H), 1.76-1.79 (m, 1H), 1.59-1.62 (m, 2H) ppm. LCMS: 95.38% (m/z): 356.87[M+H]+.

Step 5: tert-butyl (2-(((5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

To a solution of 5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde (5.3 g, 14.88 mmol) in MeOH (30 ml) was added tert-butyl methyl(2-(methylamino)ethyl)carbamate (3.36 g, 17.86 mmol) at RT. To the reaction mixture was then added anhydrous zinc chloride (0.2 g, catalytic) and TEA (10.46 ml, 74.4 mmol) and stirred for 12-15 h at 55-60° C. The reaction mixture was then cooled to 0° C. and sodium cynoborohydride (4.7 g, 74.4 mmol) was added portion wise at 0° C. and stirred for 1 h. The reaction progress was monitored by TLC. After completion of the reaction, it was diluted with water and extracted with ethyl acetate (3×50 ml). The combined organic extracts were dried over sodium sulphate and distilled under reduced pressure to get crude material. The crude product was purified by column chromatography using 20% ethyl acetate in hexane as eluent to obtain the title compound (5.4 g, Yield: 68.7%). LCMS: 93.33% (m/z): 529.42[M+H]+.

Step 6: tert-butyl (2-(((5-(3-chlorophenoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

A mixture of tert-butyl (2-(((5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (0.1 g, 0.189 mmol), 3-chlorophenol (48 mg, 0.378 mmol), potassium carbonate (52 mg, 0.75 mmol), copper powder (2.5 mg, 0.0378 mmol) and DMF (0.5 ml) in a sealed tube was heated at 100° C. under nitrogen atmosphere overnight. The cooled mixture was loaded on a silica gel column and eluted with 40% ethyl acetate in n-hexane. The obtained product was further purified by prep. TLC using 40% ethyl acetate in hexane as mobile phase to afford the pure product as oil (27 mg, yield: 27%). LCMS: 100% (m/z): 529.7 [M+H]+.

Step 7: N¹-((5-(3-chlorophenoxy)-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine (Compound 27)

To a stirred solution of tert-butyl (2-(((5-(3-chlorophenoxy)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (27 mg, 0.051 mmol) in a mixture of methanol (0.2 ml) and THF (0.1) at room temperature was added HCl in IPA (0.5 ml) and the reaction was allowed to stir at room temperature overnight. The reaction mixture was concentrated under reduced pressure to dryness and triturated with 1:1 mixture of hexane and diethylether to get pure product as dihydrochloride salt. (12.7 mg, Yield: 59.57%). ¹H-NMR (400 MHz, MeOD): δ 7.68 (d, J=8.8 Hz, 1H), 7.64 (d, J=1.6 Hz, 1H), 7.33 (t, J=8.0 Hz, 1H), 7.26 (dd, J=8.8, 2.0 Hz, 1H), 7.10 (d, J=7.6 Hz, 1H), 6.92-6.98 (m, 2H), 4.78 (s, 2H), 3.66 (s, 3H), 2.96 (s, 2H), 2.79 (s, 3H) ppm. LCMS: 95.39% (m/z): 345.2 [M+H]+, HPLC: 98.10%.

Compound 29 N¹,N²-dimethyl-N′-((5-((tetrahydro-2H-pyran-4-yl)oxy)-1H-indazol-3-yl)methyl)ethane-1,2-diamine

Step 1: tert-butyl methyl(2-(methyl((5-((tetrahydro-2H-pyran-4-yl)oxy)-1-tosyl-1H-indazol-3-yl)methyl)amino)ethyl)carbamate

tert-Butyl-(2-(((5-hydroxy-1-tosyl-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl) carbamate (0.2 g, 0.0004 mole), tetrahydro-2H-pyran-4-ol (0.05 g, 0.00049 mole), 50% tributyl phosphine (0.25 g, 0.0006 mole) and 1,1 diazocarbonyl dipiperazine (0.14 g, 0.0006 mole) were suspended in toluene (2 ml) and stirred at room temperature for 4 hrs. The reaction mixture was poured into cold water and extracted with ethyl acetate (50 ml×2). The combined organics layers were dried over sodium sulphate and concentrated under reduced pressure to get crude. material The crude product was further purified using Combi flash and the product was eluted at 25% ethyl acetate in hexane. Pure fractions were concentrated under reduce pressure to obtained pure compound (0.075 g, Yield: 31.25%).

Step 2: tert-butyl methyl(2-(methyl((5-((tetrahydro-2H-pyran-4-yl)oxy)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate

A solution of tert-butyl methyl(2-(methyl((5-((tetrahydro-2H-pyran-4-yl)oxy)-1-tosyl-1H-indazol-3-yl)methyl)amino)ethyl)carbamate (0.075 g, 0.00013 mole) and sodium hydroxide (0.026 g, 0.00065 mole) in MeOH (1 ml) was heated to 50° C. for 1 hr. The reaction mixture was diluted with water, the product extracted into ethyl acetate, the separated organic layer dried over sodium sulphate and distilled under reduced pressure to get crude material. The crude product was purified by prep TLC using 10% Methanol in DCM to get pure product (0.025 g, Yield: 46.29%).

Step 3: N¹,N²-dimethyl-N¹-((5-((tetrahydro-2H-pyran-4-yl)oxy)-1H-indazol-3-yl)methyl)ethane-1,2-diamine (Compound 29)

A solution of tert-butyl methyl(2-(methyl((5-((tetrahydro-2H-pyran-4-yl)oxy)-1H-indazol-3-yl)methyl)amino)ethyl) carbamate (0.025 g) and TFA (1 ml) in DCM (2 ml) was stirred 70° C. for 1 h. The reaction mixture was concentrated to get crude material. The crude product was purified by prep HPLC to get pure product as the TFA salt (9 mg, Yield: 47.36%). ¹H-NMR (400 MHz, MeOD): δ 7.51 (d, 1H, J=9.2 Hz), 7.37 (s, 1H), 7.16-7.19 (q, 1H), 4.49-4.56 (m, 3H), 3.97-4.02 (m, 2H), 3.6-3.66 (m, 2H), 3.46 (t, 2H, J=6.4 Hz), 3.39 (t, 2H, J=4 Hz), 2.84 (s, 3H), 2.76 (s, 3H), 2.06-2.1 (m, 2H), 1.74-1.81 (m, 2H) ppm. LCMS: 100% (m/z): 319.4 [M+1]+, HPLC: 98.5%.

Compound 36 3-((methyl(2-(methylamino)ethyl)amino)methyl)-1H-indazol-5-ol

Step 1: 5-methoxy-1H-indazole-3-carboxylic acid

5-Methoxy isatin (25 g, 0.14 mol) was dissolved in 150 ml of 1N NaOH solution and the reaction mixture stirred at 50° C. for 1 hr. The reaction mixture was cooled to room temperature and aq. H₂SO₄ (15 ml, 5% solution) was added dropwise over a period of 30 min. To the above reaction mixture aq. NaNO₂ (9.74 g, 0.14 mol in 50 ml water) was added at 0° C. and reaction mixture stirred at 0° C. for 1 hr. In another RBF, tin(II) chloride (64 g, 0.33 mol) was dissolved in 125 ml conc. HCl and cooled to 0° C. The above reaction mixture was added slowly over a period of 1 hr at 0° C. and then reaction mixture stirred at room temperature for 5 hrs. After completion of reaction, the reaction mixture was diluted with 500 ml water and the solid formed was filtered to afford pure title compound as yellowish solid. (25 g, 92.19%) LCMS: 77.96%-(m/z): 193.02 [M+H]+.

Step 2: N,5-dimethoxy-N-methyl-1H-indazole-3-carboxamide

5-Methoxy-1H-indazole-3-carboxylic acid (25 g, 0.13 mol) was dissolved in dry DMF (250 ml) and cooled to 0° C. N,O-dimethyl hydroxylamine (13.97 g, 0.143 mol) and pyridine (23.1 ml, 0.286 mol) was added and the reaction mixture stirred at 0° C. for 1 hr. EDCI-HCl (50 g, 0.26 mol) and pyridine (21 ml, 0.26 mol) was added and reaction mixture stirred at room temperature for 3 hrs. After completion of reaction, the reaction mixture was diluted with 1500 ml water and extracted with (500 ml×3)ethyl acetate. The combined organic extracts were washed with dil. HCl (250 ml×2) and distilled under reduced pressure to afford the crude material. The crude product was purified using column chromatography with the compound starting to elute at 5% MeOH in DCM to afford 18 g of pure title compound. (18 g, 58.82%).

Step 3: N,5-dimethoxy-N-methyl-1-tosyl-1H-indazole-3-carboxamide

N,5-Dimethoxy-N-methyl-1H-indazole-3-carboxamide (17 g, 0.072 mol) was dissolved in 200 ml of dry THF and cooled to 0° C. Triethylamine (20 ml, 0.144 mol) was added dropwise at 0° C. and then after 10 min tosylchloride (15.12 g, 0.079 mol) was added. This reaction mixture was stirred at 90° C. for 5 hrs. After completion of the reaction, the reaction mixture was cooled to room temperature and diluted with 200 ml water and extracted with ethyl acetate (100 ml×2). The ethyl acetate fractions were combined and distilled under reduced pressure to afford crude material. The crude product was purified by trituration with n-hexane to afford pure title compound. (25 g, 72.57%).

Step 4: 5-methoxy-1-(phenylsulfonyl)-1H-indazole-3-carbaldehyde

N,5-Dimethoxy-N-methyl-1-tosyl-1H-indazole-3-carboxamide (25 g, 0.064 mol) was dissolved in dry THF (200 ml) and cooled to −60° C. To this LAH (1.21 g, 2M in THF, 0.032 mol) was added at −60° C. slowly over a period of 30 min. The reaction mixture was stirred at −30° C. for 2 hrs. After completion of the reaction, the reaction mixture was again cooled to −78° C. and quenched with 500 ml of water. The reaction mixture was brought to room temperature and extracted with ethyl acetate (100 ml×3). The ethyl acetate fractions were combined, dried over Na₂SO₄ and distilled under reduced pressure to afford pure title compound (20 g).

Step 5: 5-hydroxy-1-(phenylsulfonyl)-1H-indazole-3-carbaldehyde

5-Methoxy-1-(phenylsulfonyl)-1H-indazole-3-carbaldehyde (20 g, 0.06 mol) was dissolved in dry DCM (300 ml) and boron tribromide (45.5 g, 0.18 mol) was added slowly over a period of 1 hr at room temperature. The reaction mixture was stirred at room temperature for 3 hrs. After completion of the reaction, the reaction mixture was diluted with 500 ml saturated NaHCO₃ and extracted with (200 ml×3)ethyl acetate. The ethyl acetate fractions were combined and distilled under reduced pressure to afford the crude material. The crude product was purified using column chromatography and compound started to elute at 15% ethyl acetate in n-hexane to afford 1 g of pure title compound. (11 g, 57.55%).

Step 6: tert-butyl (2-(((5-hydroxy-1-(phenylsulfonyl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

5-Hydroxy-1-(phenylsulfonyl)-1H-indazole-3-carbaldehyde (2 g, 0.0063 mol) and tert-butyl methyl(2-(methylamino)ethyl)carbamate (1.42 g, 0.0075 mol) were dissolved in methanol (20 ml) under nitrogen. To this reaction mixture ZnCl₂ (25 mg, cat.) and triethylamine (4.4 ml, 0.0316 mol) were added and the reaction mixture stirred at 50° C. overnight. The reaction mixture was cooled to 0° C. and sodium cyanoborohydride (2.02 g, 0.0316 mol) added. This reaction mixture was stirred at room temperature for 3 hrs. After completion of the reaction, the reaction mixture was diluted with 50 ml water and extracted with (20 ml×3)ethyl acetate. The ethyl acetate fractions were combined and distilled under reduced pressure to afford the crude material. The crude product was purified using column chromatography and the compound started eluting at 50% ethyl acetate in n-hexane to afford 1.3 g of pure title compound. (1.3 g, 41.40%).

Step 7: tert-butyl (2-(((5-hydroxy-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl) carbamate

tert-Butyl (2-(((5-hydroxy-1-(phenylsulfonyl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (150 mg, 0.000314 mol) was dissolved in methanol (2 ml) and NaOH (64 mg, 0.0015 mol) was added. The reaction mixture was stirred at 50° C. for 2 hrs. After completion of the reaction, the excess methanol was distilled off and to the residue was added 10 ml water. The mixture was extracted with (20 ml×2)ethyl acetate and the combined ethyl acetate fractions were combined and distilled under reduced pressure to afford pure compound (70 mg, 66.22%).

Step 8: 3-((methyl(2-(methylamino)ethyl)amino)methyl)-1H-indazol-5-ol (Compound 36)

tert-Butyl (2-(((5-hydroxy-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (70 mg) was dissolved in 2 ml methanolic HCl and the reaction mixture stirred at 40° C. for 3 hrs. After completion of the reaction, the excess methanol was distilled off and the crude material was triturated with diethyl ether to afford pure title compound as HCl salt. (40 mg, 81.56%), LCMS: 99.05% (m/z) 235.48 (M++1), HPLC: 98.67%. ¹H-NMR (400 MHz, DMSO-d6) δ 7.46-7.44 (d, 1H), 7.18 (s, 1H), 7.03-6.99 (d, 1H), 4.69 (s, 2H), 3.39-3.38 (m, 4H), 3.21 (m, 2H), 2.83-2.77 (m, 2H), 2.55-2.50 (m, 6H) ppm.

Compound 41 5-((3-((methyl(2-(methylamino)ethyl)amino)methyl)-1H-indazol-4-yl)oxy)pentane-1,2-diol

Step 1: pentane-1,2,5-triol

Pent-4-en-1-ol (150 mg, 1.74 mmol) was dissolved in THF (2 ml) and 4-methyl morpholine-N-oxide (190 mg, 1.74 mmol) and OsO₄ (0.1 ml-5% aqueous solution) were added at room temperature and the reaction mixture allowed to stir for 3 hours. The reaction mixture was then concentrated under reduced pressure to get crude material which was used as such for the next step. (170 mg, Yield: 81.31%).

Step 2: 3-(2,2-dimethyl-1,3-dioxolan-4-yl)propan-1-ol

Pentane-1,2,5-triol (170 mg, 0.81 mmol) and PTSA (30 mg, 0.20 mmol) were dissolved in 2,2-dimethoxy propane (2.5 ml) and allowed to stir at ambient temperature for 3 hr. The reaction mixture was quenched with 50 ml of water and extracted with ethyl acetate (50 ml×2). The combined organic extracts were dried over sodium sulfate and concentrated under reduced pressure to give the crude material which was purified by Combi-flash using 50% ethyl acetate in hexane as eluent. Pure fractions were concentrated to give title compound (80 mg, Yield: 35.39%).

Step 3: 3-(2,2-dimethyl-1,3-dioxolan-4-yl)propyl methanesulfonate

3-(2,2-Dimethyl-1,3-dioxolan-4-yl)propan-1-ol (80 mg, 0.50 mmol) was dissolved in THF (2 ml) and TEA (151 mg, 1.5 mmol) was added at room temperature. The reaction mixture was cooled to 0° C. temperature and a solution of methanesulfonyl chloride (68 mg, 0.60 mmol) in THF (0.5 ml) was added dropwise. The reaction mixture was allowed to stir at ambient temperature for 2 hrs. The reaction mixture was then quenched with ice cold water (50 ml) and extracted with ethyl acetate twice. The combined organic extracts were dried over sodium sulfate and concentrated under reduce pressure to give the title compound (70 mg, 58.82%).

Step 4: tert-butyl 3-(((2-((tert-butoxycarbonyl)(methyl)amino)ethyl)(methyl)amino)methyl)-4-(3-(2,2-dimethyl-1,3-dioxolan-4-yl)propoxy)-1H-indazole-1-carboxylate

tert-Butyl 3-(((2-((tert-butoxycarbonyl)(methyl)amino)ethyl)(methyl)amino)methyl)-4-hydroxy-1H-indazole-1-carboxylate (150 mg, 0.34 mmol) was dissolved in acetonitrile (2 ml) and 3-(2,2-dimethyl-1,3-dioxolan-4-yl)propyl methanesulfonate (70 mg, 0.34 mmol) was added followed by cesium carbonate (169 mg, 0.51 mmol). The reaction mixture was heated at 80° C. for 1 hr. The reaction mixture was concentrated under vacuum and added to ice cold water. It was extracted twice using DCM (50 ml). The combined organic layers were dried over sodium sulfate and concentrated under reduced pressure to give crude product which was purified using column chromatography. The product eluted at 50% ethyl acetate in hexane. The pure fractions were concentrated to give the title compound (90 mg, 45.45%). LCMS: 95.46% (m/z): 577.78 [M+1]⁺.

Step 5: 5-((3-((methyl(2-(methylamino)ethyl)amino)methyl)-1H-indazol-4-yl)oxy)pentane-1,2-diol (Compound 41)

tert-Butyl 3-(((2-((tert-butoxycarbonyl)(methyl)amino)ethyl)(methyl)amino)methyl)-4-(3-(2,2-dimethyl-1,3-dioxolan-4-yl)propoxy)-1H-indazole-1-carboxylate (90 mg, 0.15 mmol) was dissolved in DCM (2 ml) and trifluoroacetic acid (0.3 ml, 34.4 mmol) added at room temperature. The reaction mixture was allowed to stir at ambient temperature for 5 hrs. It was then concentrated under vacuum to get the crude material which was further purified by trituration with diethyl ether to give title compound as the TFA salt (55 mg, 63.95%). ¹H-NMR (400 MHz, MeOD): δ 7.37 (t, J=16 Hz, 1H), 7.15 (dd, J=8.0 Hz, 1H), 6.67 (dd, J=12 Hz, 1H), 4.27-4.28 (m, 2H), 3.73-3.78 (m, 1H), 3.57-3.65 (m, 1H), 3.02 (d, J=4.0 Hz, 3H), 2.81 (d, J=2.4 Hz 3H), 2.13-2.17 (m, 1H), 2.02-2.06 (m, 2H), 1.68-1.82 (m, 2H) ppm. LCMS: 94.96 (m/z): 336.99 [M+H]⁺, HPLC: 96.75%.

Compound 42 N¹-((5-isopropyl-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine

Step 1: tert-butyl (2-(((5-isopropyl-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

To a suspension of 10% Pd/C (0.05 g) in methanol (3 ml), tert-butyl methyl(2-(methyl((5-(prop-1-en-2-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)amino)ethyl) carbamate (0.1 g) in methanol (2 ml) was added under a nitrogen atmosphere. Hydrogen gas was introduced for 3 hrs at room temperature. The reaction mixture was filtered through a Celite-band which was then washed with methanol. The filtrate was concentrated under reduced pressure at 40° C. to get a solid (55 mg, Yield: 55%).

Step 2: N¹-((5-isopropyl-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine (Compound 42)

A solution of tert-butyl (2-(((5-isopropyl-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (55 mg, 0.123 mmol) in dioxane-HCl (5 mL) was stirred at room temperature for 1 h. The reaction mixture was concentrated and purified by prep HPLC to get the pure product as HCl salt (20 mg, Yield=62.5%). ¹H-NMR (400 MHz, MeOD): δ 7.72 (s, 1H), 7.54 (d, 1H, J=8.8 Hz), 7.42 (d, 1H, J=7.2 Hz), 4.92 (s, 2H), 3.51 (s, 3H), 3.33 (s, 2H), 2.94 (s, 2H), 2.83 (s, 2H), 2.73 (s, 3H), 1.3-1.37 (m. 7H) ppm. LCMS: 100% m/z 259.4[M+1]⁺, HPLC: 95.2%.

Compound 43 N¹-((5-(3-azaspiro[5.5]undecan-3-yl)-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine

Step 1: 3-azaspiro[5.5]undecane

To a solution of 3-azaspiro[5.5]undecane-2,4-dione (1 g, 0.0055 mole) in THF (1 mL), 1M LAH in THF (28 mL, 0.0276 mole) was added slowly at 0° C. The reaction mixture was allowed to come to room temperature and stirred for 15 minute, the temperature was then raised to 110° C. and stirred at that temperature overnight. After completion of the reaction, the reaction mixture was quenched in saturated NH₄Cl solution. The inorganic salts formed were filtered through Celite and the filtrate concentrated under reduced pressure to remove THF. The aqueous layer was washed with ethyl acetate, then basified with 10% NaOH solution and again extracted with ethyl acetate. The combined organic extracts were dried over anhydrous sodium sulfate and concentrated to give product (0.6 g, Yield: 71%) which was used in the next step without any further purification. (LCMS: Mass part of LCMS shows 84.83% of m/z-154 [M+H]⁺).

Step 2: N¹-((5-(3-azaspiro[5.5]undecan-3-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)-N²-((l1-methyl)(l1-oxidanyl)boranyl)-N¹,N²-dimethylethane-1,2-diamine

To a solution of N¹-((11-methyl)(11-oxidanyl)boranyl)-N²-((5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine (0.150 g, 0.284 mmole) and 3-azaspiro[5.5]undecane (0.173 g, 1.136 mmole) in DMSO (1 ml) were added K₂CO₃ (0.156 g, 1.136 mmole), CuI (0.008 g, 0.0426 mmole) and N,N-dimethyl glycine (0.009 g, 0.0852 mmole). The reaction mixture was stirred at 120° C. overnight. After completion of the reaction it was poured into water and extracted with ethyl acetate. The organic layer was washed with brine, dried over anhydrous sodium sulfate and evaporated under reduced pressure to get crude product. Crude product was purified by Combi flash, the product eluted at 40% of ethyl acetate in n-hexane. (0.076 g, Yield: 48.1%); LCMS: 74.76% (m/z): 554.3 [M+H]⁺.

Step 3: N¹-((5-(3-azaspiro[5.5]undecan-3-yl)-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine (Compound 43)

To a solution of N¹-((5-(3-azaspiro[5.5]undecan-3-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)-N²-((l1-methyl)(l1-oxidanyl)boranyl)-N¹,N²-dimethylethane-1,2-diamine (0.168 g) in methanol (0.5 mL), HCl in IPA (1 mL) was added and reaction mixture stirred at room temperature overnight. The reaction mixture was concentrated under reduced pressure, triturated with n-hexane and purified by prep HPLC using Water/ACN as a mobile phase and 0.1% TFA as modifier to get pure product as the TFA Salt (0.032 g, Yield: 25.39%). ¹H-NMR (400 MHz, DMSO): δ 13.64 (s, 1H), 10.70 (s, 1H), 8.79 (s, 2H), 7.50-7.85 (m, 3H), 5.22 (s, 2H), 4.68 (s, 2H) 2.80 (s, 2H), 2.61 (s, 2H), 1.71 (s, 4H), 1.44 (s, 9H) ppm. ¹H-NMR (400 MHz, DMSO-D2O exchange): δ 8.17 (s, 1H), 7.64-7.76 (m, 2H), 4.72 (s, 2H), 3.35-3.48 (m, 7H), 2.86 (s, 3H), 2.61 (s, 3H), 1.79 (s, 3H), 1.21 (s, 9H) ppm. LCMS: 100% m/z=370.0[M+1]⁺, HPLC: 99.12%.

Compound 44 N¹,N²-dimethyl-N-((5-(tetrahydro-2H-pyran-4-yl)-1H-indazol-3-yl)methyl)ethane-1,2-diamine

Step 1: N-methoxy-N-methyl-1H-indazole-3-carboxamide

To a stirred solution of 1H-indazole-3-carboxylic acid (23 g, 141 mmol) in THF (1400 ml) was added N,O-dimethylhydroxylamine.HCl (16.5 g, 169.2 mmol) followed by dry pyridine (13.6 ml, 169.2 mmol) at 0° C. The reaction mixture was allowed to stir at room temperature for 2 hrs which was followed by addition of EDC.HCl (32.8 g, 211.5 mmol) and dry pyridine (28.5 ml, 352.5 mmol). The reaction mixture was allowed to stir overnight at room temperature. The reaction mixture was concentrated to dryness and 1500 ml of water was added. The resulting mixture was allowed to stir at RT for 30 mins. The precipitates were filtered and washed with diethyl ether to get the pure product as a yellow solid. (22 g, yield: 75.6%).

Step 2: 5-iodo-N-methoxy-N-methyl-1H-indazole-3-carboxamide

To a solution of N-methoxy-N-methyl-1H-indazole-3-carboxamide (10.2 g 49.7 mmol) in 180 ml of DCM was added bis(trifluoroacetoxy)iodobenzene (23.4 g, 54.67 mmol) at room temperature. After stirring for 5 min, a solution of iodine (7.6 g, 29.82 mmol) in DCM (400 ml) was added dropwise over a period of 0.5 h and stirring continued for 8 h. The reaction progress was monitored by TLC. After completion of the reaction, it was diluted with a saturated solution of sodium thiosulphate and extracted with DCM (3×150 ml). The combined organic extracts were dried over sodium sulphate and distilled under reduced pressure to get the crude material. The crude product was purified by trituration with hexane to obtain the title compound (12.2 g, Yield: 74.13%). H-NMR (400 MHz, DMSO-d₆): δ 13.81 (s, 1H), 8.40 (s, 1H), 7.66-7.67 (d, J=1.6 Hz, 1H), 7.49-7.51 (d, J=8.8 Hz, 1H), 3.78 (s, 3H), 3.45 (s, 3H) ppm. LCMS: 68.17% (m/z): 331.91[M+H]⁺.

Step 3: 5-iodo-N-methoxy-N-methyl-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carboxamide

To a solution of 5-iodo-N-methoxy-N-methyl-1H-indazole-3-carboxamide (1.0 g, 3.02 mmol) in 30 ml of DCM was added PTSA (0.575 g, 3.02 mmol) and the reaction mixture stirred vigorously for 10 min at RT. Then 3,4-dihydro-2H-pyran (0.635 g, 7.55 mmol) was added dropwise and stirred for another 2 h. The reaction progress was monitored by TLC. After completion of the reaction, it was diluted with water and extracted with DCM (3×50 ml). The combined organic extracts were dried over sodium sulphate and distilled under reduced pressure to get the crude material. The residue was purified by column chromatography using 3-4% MeOH: DCM as eluent to obtain the title compound (1.0 g, Yield: 80%). LCMS: 83.73% (m/z): 416.14[M+H]⁺.

Step 4: 5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde

To a solution of 5-iodo-N-methoxy-N-methyl-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carboxamide (0.5 g, 1.2 mmol) in 5 ml of dry THF at −50° C. under an argon atmosphere was added dropwise 1M LAH in THF (0.3 mmol). The reaction mixture was stirred for 1 h at −50° C. and the reaction progress monitored by TLC. After completion of the reaction, it was poured in saturated ammonium chloride solution and extracted with ethyl acetate (3×25 ml). The combined organic extracts were dried over sodium sulphate and distilled under reduced pressure to give the title compound (0.4 g, Yield: 93%). ¹H-NMR (400 MHz, DMSO-d₆): δ 10.17 (s, 1H), 8.50 (s, 1H), 7.78-7.86 (m, 2H), 6.07 (dd, J=9.2 Hz, 2.0 1H), 3.78-3.91 (m, 2H), 2.38-2.40 (m, 1H), 2.05-2.08 (m, 2H), 1.76-1.79 (m, 1H), 1.59-1.62 (m, 2H) ppm. LCMS: 95.38% (m/z): 356.87[M+H]⁺

Step 5: tert-butyl (2-(((5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

To a solution of 5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazole-3-carbaldehyde (5.3 g, 14.88 mmol) in MeOH (30 ml) was added tert-butyl methyl(2-(methylamino)ethyl)carbamate (3.36 g, 17.86 mmol) at RT. To the reaction mixture was then added anhydrous zinc chloride (0.2 g, Catalytic) and TEA (10.46 ml, 74.4 mmol) and stirring continued for 12-15 h at 55-60° C. The reaction mixture was then cooled to 0° C. and sodium cyanoborohydride (4.7 g, 74.4 mmol) was added portion wise at 0° C. and stirring continued for 1 h. The reaction progress was monitored by TLC. After completion of the reaction, it was diluted with water and extracted with ethyl acetate (3×50 ml). The combined organic extracts were dried over sodium sulphate and distilled under reduced pressure to get the crude material. The crude product was purified by column chromatography using 20% ethyl acetate in hexane as eluent to obtain the title compound (5.4 g, Yield: 68.7%). LCMS: 93.33% (m/z): 529.42[M+H]⁺.

Step 6: tert-butyl (2-(((5-(3,6-dihydro-2H-pyran-4-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

tert-Butyl (2-(((5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (400 mg, 0.00075 mol) and tert-butyl methyl(2-(methylamino)ethyl)carbamate (190 mg, 0.0009 mol) were dissolved in dry dioxane and purged with argon for 10 min. Potassium carbonate (156 mg, 0.0011 mol) and Pd(PPh₃)₄ (18 mg, 0.000015 mol) was added and the reaction mixture was again purged with argon for 10 min. The reaction mixture was stirred at 60° C. for 4 hrs. After completion of reaction, the reaction mixture was cooled to room temperature, diluted with 20 ml water and extracted with ethyl acetate (20 ml×3). The ethyl acetate fractions were combined, dried over Na₂SO₄ and distilled under reduced pressure to afford the crude material. The crude product was purified by column chromatography and product started eluting at 50% ethyl acetate in n-hexane. Evaporation of the appropriate fractions afforded 250 mg of pure title compound. (250 mg, 68.15%) LCMS: 92.69% (m/z) 484.47 (M++1).

Step 7: tert-butyl methyl(2-(methyl((1-(tetrahydro-2H-pyran-2-yl)-5-(tetrahydro-2H-pyran-4-yl)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate N,5-dimethoxy-N-methyl-1H-indazole-3-carboxamide

To a solution of tert-butyl (2-(((5-(3,6-dihydro-2H-pyran-4-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (250 mg) in 5 ml methanol, 10% Pd/C (100 mg) was added and hydrogen gas was introduced into the reaction mixture for 2 hrs. After completion of the reaction, the reaction mixture was passed through a Celite bed and the methanol was distilled under reduced pressure to give 200 mg of title compound.

Step 8: N¹,N²-dimethyl-N¹-((5-(tetrahydro-2H-pyran-4-yl)-1H-indazol-3-yl)methyl)ethane-1,2-diamine (Compound 44)

tert-Butyl methyl(2-(methyl((1-(tetrahydro-2H-pyran-2-yl)-5-(tetrahydro-2H-pyran-4-yl)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate N,5-dimethoxy-N-methyl-1H-indazole-3-carboxamide (200 mg) was dissolved in 3 ml IPA-HCl and the reaction mixture stirred at 50° C. for 5 hrs. After completion of reaction the IPA was distilled off and the crude material purified using prep HPLC (0.1% TFA in ACN+H₂O). Evaporation of prep HPLC fractions afforded the pure title compound as TFA salt. (50 mg, 40.23%), LCMS: 99.29% (m/z) 303.14 (M++1), HPLC: 99.17%. ¹H-NMR (400 MHz, DMSO-d6) δ 13.42 (s, 1H), 10.50 (s, 1H), 8.69 (s, 2H), 7.79 (s, 1H), 7.55-7.53 (d, 1H), 7.38-7.36 (d, 1H), 4.67 (s, 2H), 4.14-3.97 (m, 9H), 3.50-3.47 (m, 3H), 2.92-2.88 (m, 3H), 2.78 (s, 3H), 2.66-2.50 (m, 4H) ppm.

Compound 46 N¹,N²-dimethyl-N¹-((5-(piperidin-1-yl)-1H-indazol-3-yl)methyl)ethane-1,2-diamine

Step 1: tert-butyl methyl(2-(methyl((5-(piperidin-1-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate

To a solution of tert-butyl (2-(((5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (200 mg, 0.38 mmol) in piperidine (2 ml) was added NiCl₂.H₂O (0.450 g, 3.8 mmol) at RT in a 10 ml microwave vial. The reaction was irradiated for 0.5 h at 150° C. in an Anton Paar microwave synthesizer. The reaction progress was monitored by TLC. After completion of reaction, the reaction was diluted with water and extracted with ethyl acetate. The combined organic layers were dried over sodium sulphate and evaporated under vacuum to obtain the crude compound. This was purified by flash column chromatography with the product eluting at 2.5% MeOH in DCM. The pure fractions were evaporated under reduced pressure to give the title compound (150 mg, yield 92%). LCMS (m/z): 88.89%, 486.47 [M+1]⁺.

Step 2: N¹,N²-dimethyl-N¹-((5-(piperidin-1-yl)-1H-indazol-3-yl)methyl)ethane-1,2-diamine (Compound 46)

To a solution of tert-butyl methyl(2-(methyl((5-(piperidin-1-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)amino)ethyl)carbamate (170 mg) in 5 ml of 1,4-dioxane at 20° C. was added dropwise 1M HCl in dioxane (5 ml). The reaction mixture was stirred for 6 h at RT. After completion of the reaction, it was distilled under reduced pressure and the crude material was purified by trituration with diethyl ether to get the title compound (46.2 mg, Yield: 43.8%). ¹H-NMR (400 MHz, MeOD): δ 8.68 (s, 1H), 7.83-7.86 (d, J=9.2 Hz, 1H), 7.76-7.78 (d, J=9.6 Hz, 1H), 3.50-3.80 (m, 8H), 3.03 (s, 3H), 2.82 (s, 3H), 2.01-2.15 (m, 4H), 1.74-1.79 (m, 2H) ppm. LCMS: 91.54% (m/z): 301.94[M+H]⁺, HPLC: 91.32%.

Compound 47 N¹-((5-cyclohexyl-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine

Step 1: tert-Butyl(2-(((5-(cyclohex-1-en-1-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

To a solution of tert-butyl (2-(((5-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (250 mg, 0.473 mmol) in dioxane (4 ml) was added 2-(cyclohex-1-en-1-yl)-4,4,5,5-tetramethyl-1,3,2-dioxaborolane (118 mg, 0.57 mmol) and K₂CO₃ (196 mg, 1.419 mmol) in 1 ml water. The reaction mixture was degassed with argon for 0.5 h and then tetrakis(triphenylphosphine)palladium(0) (38 mg, 0.033 mmol) added. The resulting mixture was heated for 5 hrs at 60° C. After completion of the reaction, the reaction mixture was poured into water (20 mL) and extracted with EtOAc (20 mL×3). The combined organic layers were washed with brine (20 mL), dried over anhydrous sodium sulphate, filtered and evaporated under reduced pressure. The residue was purified by column chromatography using neutral alumina as a stationary phase and 25%-30% ethyl acetate in hexane as eluent to obtain the title compound (130 mg, yield 57%). LCMS (m/z): 95.63%, 483.31 [M+1]⁺.

Step 2: tert-butyl(2-(((5-cyclohexyl-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

To a solution of tert-butyl (2-(((5-(cyclohex-1-en-1-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (80 mg) in MeOH (5 ml) was added 10% Pd—C (40 mg) and hydrogen gas was introduced for 2 h at RT. The reaction progress was monitored by TLC. After completion of reaction, the reaction was filtered and evaporated to obtain the title compound (60 mg, yield 74.7%). LCMS (m/z): 100%, 485.31 [M+1]⁺.

Step 3: N¹-((5-cyclohexyl-1H-indazol-3-yl)methyl)-N¹,N²-dimethylethane-1,2-diamine (Compound 47)

To a solution of tert-butyl(2-(((5-cyclohexyl-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (60 mg) in 5 ml of 1,4-dioxane at 20° C. was added dropwise HCl in dioxane (5 ml). The reaction mixture was stirred for 6 h at RT. After completion of the reaction, it was concentrated under reduced pressure and the crude product purified by reverse phase prep HPLC using Water/ACN as mobile phase and 0.1% TFA as modifier. Lyophilization of the prep fractions afforded the title compound as the TFA salt (23.2 mg, Yield: 40%). ¹H-NMR (400 MHz, MeOD): δ 7.73 (s, 1H), 7.53 (d, J=8.4 Hz, 1H), 7.40 (dd, J=10.0, 1.2 Hz, 1H), 4.83 (s, 2H), 3.57-3.60 (m, 4H), 3.02 (s, 3H), 2.80 (s, 3H), 1.80-1.95 (m, 6H), 1.45-1.62 (m, 5H) ppm. LCMS: 97.79% (m/z): 301.14[M+H]⁺, HPLC: 97.34%.

Compound 58 1-(4-((3-((methyl(2-(methylamino)ethyl)amino)methyl)-1H-indazol-5-yl)oxy)piperidin-1-yl)ethan-1-one

Step 1: tert-butyl (2-(((5-((1-acetylpiperidin-4-yl)oxy)-1-tosyl-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

To a solution of 1-acetylpiperidin-4-yl methanesulfonate (0.1 g, 0.415 mmole) in acetonitrile (3 ml) was added cesium carbonate (0.29 g, 0.830 mmole). tert-Butyl (2-(((5-hydroxy-1-tosyl-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (0.22 g, 0.415 mmole) was added and the reaction mixture stirred overnight at reflux temperature. The cooled reaction mixture was poured into water (15 ml) and extracted with ethyl acetate (15 ml×3). The combined organic extracts were dried over sodium sulphate and concentrated under reduced pressure to get title compound (0.064 g, Yield: 23.07%) LCMS: 61.72% (m/z): 614.80 [M+1]+.

Step 2: tert-butyl (2-(((5-((1-acetylpiperidin-4-yl)oxy)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

A solution of tert-butyl (2-(((5-((1-acetylpiperidin-4-yl)oxy)-1-tosyl-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (0.064 g, 0.00104 mole) and sodium hydroxide (0.017 g, 0.00417 mole) in MeOH (1 ml) was heated to 500° C. for 1 hr. The reaction mixture was diluted with water, the product extracted in ethyl acetate, the organic layer dried over sodium sulphate and distilled under reduced pressure to get crude product (0.050 g, Yield: quantitative).

Step 3: 1-(4-((3-((methyl(2-(methylamino)ethyl)amino)methyl)-1H-indazol-5-yl)oxy)piperidin-1-yl)ethan-1-one (Compound 58)

To a solution of tert-butyl (2-(((5-((1-acetylpiperidin-4-yl)oxy)-1H-indazol-3-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate (0.050 g) in DCM (2 ml) was added TFA (1 ml) and the reaction mixture stirred at 400 C for 1 h. The reaction mixture was concentrated to get crude material. The crude product was purified by prep HPLC using water/ACN as a mobile phase and 0.1% TFA as modifier to get the title compound as a TFA salt (9 mg, Yield: 23.01%). ¹H-NMR (400 MHz, MeOD): δ 7.50 (d, 1H, J=9.2 Hz), 7.38 (s, 1H), 7.37-7.20 (q, 1H), 4.70 (m, 2H), 4.47 (s, 2H), 3.84-3.81 (m, 2H), 3.59-3.51 (m, 2H), 3.49-3.40 (m, 2H), 2.75 (s, 6H), 2.15 (s, 3H), 2.01-1.95 (m, 2H), 1.87-1.78 (m, 2H) ppm. LCMS: 98.33% (m/z): 360.08 [M+1]+. HPLC: 99.35%.

Synthesis of Intermediates Intermediate I tert-butyl (2-(((3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazol-4-yl)methyl)(methyl)amino)ethyl)carbamate

Step 1: tert-butyl (2-(((3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazol-4-yl)methyl)(methyl)amino)ethyl)carbamate

A mixture of 3-iodo-1-(oxan-2-yl)-1H-pyrazole-4-carbaldehyde (3.2 g, 10.45 mmol, 1.00 equiv), tert-butyl N-[2-(methylamino)ethyl]carbamate (2.2 g, 12.63 mmol, 1.21 equiv) and NaBH(OAc)₃ (6.65 g, 31.38 mmol, 3.00 equiv) in dichloroethane (30 mL) was stirred for 2 h at room temperature. The reaction was quenched with 50 mL of saturated aqueous sodium bicarbonate solution. The resulting mixture was extracted with 3×200 mL of dichloromethane. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 30-100% ethyl acetate in petroleum ether to give 4.05 g (83%) of tert-butyl (2-(((3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazol-4-yl)methyl)(methyl)amino)ethyl)carbamate as a light yellow oil. ¹H-NMR (300 MHz, CDCl₃): δ 7.48 (s, 1H), 5.35-5.30 (m, 1H), 4.13-4.03 (m, 1H), 3.71-3.63 (m, 1H), 3.36 (s, 2H), 3.26-3.25 (m, 2H), 2.52-2.49 (m, 2H), 2.21 (s, 3H), 2.09-2.01 (m, 3H), 1.68-1.58 (m, 3H), 1.44 (s, 9H) ppm. LCMS (method C, ESI): RT=0.58 min, m/z=465.0 [M+H]⁺.

Intermediate II tert-butyl (2-(((3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazol-4-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

Step 1: ethyl 3-iodo-1H-pyrazole-4-carboxylate

To a stirred solution of ethyl 3-amino-1H-pyrazole-4-carboxylate (10 g, 64.45 mmol, 1.00 equiv) in 50% sulfuric acid (90 mL) at 5° C. was added dropwise a solution of NaNO₂ (7.4 g, 107.25 mmol, 1.66 equiv) in water (15 mL). The reaction was stirred at 5° C. for another 30 min. A solution of KI (32.1 g, 193.37 mmol, 3.00 equiv) in water (15 mL) was added dropwise at 5° C. The reaction was allowed to stir at 5° C. for 1 h and then quenched by the addition of 50 mL of water. The precipitate was collected by filtration and then dissolved in 150 mL of ethyl acetate. The resulting solution was washed sequentially with 1×100 mL of saturated Na₂SO₃ solution, 1×100 mL of saturated sodium bicarbonate solution and 1×100 mL of brine. The organic layer was dried over anhydrous sodium sulfate and concentrated under vacuum to give 10.8 g (63%) of ethyl 3-iodo-1H-pyrazole-4-carboxylate as a yellow solid. ¹H-NMR (300 MHz, CDCl₃): δ 8.18 (s, 1H), 4.38-4.29 (m, 2H), 1.41-1.33 (m, 3H) ppm. LCMS (method B, ESI): RT=1.36 min, m/z=267.0 [M+H]⁺.

Step 2: ethyl 3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazole-4-carboxylate

A solution of ethyl 3-iodo-1H-pyrazole-4-carboxylate (10.8 g, 40.60 mmol, 1.00 equiv), 3,4-dihydro-2H-pyran (10 g, 118.88 mmol, 2.93 equiv) and TsOH (780 mg, 4.53 mmol, 0.11 equiv) in THF (100 mL) was stirred for 2 h at 60° C. The reaction mixture was cooled to room temperature and quenched by the addition of 100 mL of saturated sodium bicarbonate solution. The resulting solution was extracted with 2×80 mL of dichloromethane. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with ethyl acetate/petroleum ether (1:20) to give 13 g (91%) of ethyl 3-iodo-1-(oxan-2-yl)-1H-pyrazole-4-carboxylate as a yellow oil. ¹H-NMR (400 MHz, CDCl₃): δ 8.04 (s, 1H), 5.40-5.38 (m, 1H), 4.34-4.29 (m, 2H), 4.08-4.05 (m, 1H), 3.73-3.70 (m, 1H), 2.07-1.98 (m, 3H), 1.69-1.62 (m, 3H), 1.39-1.32 (m, 3H) ppm. LCMS (method C, ESI): RT=1.53 min, m/z=351.0 [M+H]⁺.

Step 3: 3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazole-4-carboxylic acid

To a solution of ethyl 3-iodo-1-(oxan-2-yl)-1H-pyrazole-4-carboxylate (85 g, 242.75 mmol, 1.00 equiv) in THF (300 mL) and methanol (300 mL) was added a solution of LiOH (17.5 g, 730.69 mmol, 3.01 equiv) in water (400 mL). The resulting solution was stirred at room temperature overnight and then concentrated under vacuum to remove the organic solvent. The resulting solution was diluted with 400 mL of H₂O and then acidified to pH 6.0 with 1M hydrochloric acid. The mixture was extracted with 3×800 mL of dichloromethane. The combined organic layers was washed with 3×1000 mL of brine, dried over anhydrous sodium sulfate and concentrated under vacuum to give 75 g (96%) of 3-iodo-1-(oxan-2-yl)-1H-pyrazole-4-carboxylic acid as an off-white solid. LCMS (method D, ESI): RT=1.23 min, m/z=323.0 [M+H]⁺.

Step 4: (3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazol-4-yl)methanol

To a solution of 3-iodo-1-(oxan-2-yl)-1H-pyrazole-4-carboxylic acid (28 g, 86.93 mmol, 1.00 equiv) in anhydrous THF (300 mL) maintained under nitrogen at 5° C. was added a 1M solution of BH₃ in THF (300 mL) dropwise with stirring. The reaction was stirred overnight at room temperature and then quenched by the addition of 300 mL of saturated NH₄Cl solution. The resulting mixture was extracted with 3×1000 mL of dichloromethane. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with ethyl acetate/petroleum ether (1:1) to give 12.67 g (47%) of (3-iodo-1-(oxan-2-yl)-1H-pyrazol-4-yl)methanol as a white solid. ¹H-NMR (400 MHz, DMSO-d6): δ 7.73 (s, 1H), 5.37-5.34 (m, 1H), 4.92 (s, 1H), 4.20 (d, J=3.6 Hz, 2H), 3.89-3.88 (m, 1H), 3.65-3.57 (m, 1H), 2.09-2.00 (m, 1H), 1.99-1.90 (m, 2H), 1.69-1.61 (m, 1H), 1.49-1.46 (m, 2H) ppm. LCMS (method A, ESI): RT=1.16 min, m/z=309.0 [M+H]⁺.

Step 5: 3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazole-4-carbaldehyde

Into a 250-mL 3-necked round-bottom flask purged and. To a stirred solution of oxalyl chloride (18.576 g, 146.35 mmol, 3.01 equiv) in anhydrous dichloromethane (300 mL) maintained under nitrogen at −78° C. was added DMSO (15.138 g, 193.75 mmol, 3.98 equiv) dropwise. The reaction mixture was stirred at −65° C. for 30 min. A solution of (3-iodo-1-(oxan-2-yl)-1H-pyrazol-4-yl)methanol (15.0 g, 48.68 mmol, 1.00 equiv) in dichloromethane (100 mL) was then added dropwise at −65° C. and the reaction was stirred for another 60 min at −65° C. Triethylamine (40.6 mL) was added dropwise at −65° C. and the reaction was stirred for 30 min at −65° C. The reaction was warmed to 0° C. then quenched by the addition of 100 mL of saturated NH₄Cl solution. The resulting mixture was extracted with 3×400 mL of dichloromethane. The combined organic layers was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with ethyl acetate/petroleum ether (1:20) to give 13.48 g (90%) of 3-iodo-1-(oxan-2-yl)-1H-pyrazole-4-carbaldehyde as a golden oil. ¹H-NMR (300 MHz, DMSO-d6): δ 9.69 (s, 1H), 8.57 (s, 1H), 5.49 (dd, J=2.7 Hz, 9.9 Hz, 1H), 3.95-3.91 (m, 1H), 3.68-3.62 (m, 1H), 2.11-2.01 (m, 3H), 1.69-1.62 (m, 3H) ppm. LCMS (method A, ESI): RT=1.35 min, m/z=307.0 [M+H]⁺.

Step 6: tert-butyl (2-(((3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazol-4-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate

A mixture of 3-iodo-1-(oxan-2-yl)-1H-pyrazole-4-carbaldehyde (21.5 g, 70.24 mmol, 1.00 equiv), tert-butyl N-methyl-N-(2-(methylamino)ethyl)carbamate (20 g, 106.23 mmol, 1.51 equiv) and NaBH(OAc)₃ (29.8 g, 137.98 mmol, 1.96 equiv) in dichloroethane (300 mL) was stirred for 1 h at room temperature. The reaction was diluted with 300 mL of dichloromethane and then washed with 3×300 mL of brine. The organic layer was dried over anhydrous sodium sulfate and concentrated under vacuum. The residue was purified on a silica gel column eluted with 0-7% methanol in dichloromethane to give 31 g (92%) of tert-butyl (2-(((3-iodo-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazol-4-yl)methyl)(methyl)amino)ethyl)(methyl)carbamate as a yellow oil. ¹H-NMR (300 MHz, CDCl₃): δ 7.62 (s, 1H), 5.34-5.30 (m, 1H), 4.06-4.02 (m, 1H), 3.68-3.62 (m, 1H), 3.42-3.38 (m, 4H), 2.85 (s, 4H), 2.62-2.53 (m, 2H), 2.47-2.46 (m, 2H), 2.13-1.97 (m, 3H), 1.74-1.69 (m, 3H), 1.46 (s, 9H) ppm. LCMS (method A, ESI): RT=1.17 min, m/z=479.0 [M+H]⁺.

Biological Methods PRMT1 Biochemical Assay

General Materials.

S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), bicine, Tween20, dimethylsulfoxide (DMSO), bovine skin gelatin (BSG), and Tris(2-carboxyethyl)phosphine hydrochloride solution (TCEP) were purchased from Sigma-Aldrich at the highest level of purity possible. ³H-SAM was purchase from American Radiolabeled Chemicals with a specific activity of 80 Ci/mmol. 384-well streptavidin Flashplates were purchased from PerkinElmer.

Substrates.

Peptide representative of human histone H4 residues 36-50 was synthesized with an N-terminal linker-affinity tag motif and a C-terminal amide cap by 21^(st) Century Biochemicals. The peptide was purified by high-performance liquid chromatography (HPLC) to greater than 95% purity and confirmed by liquid chromatography mass spectrometry (LC-MS). The sequence was Biot-Ahx-RLARRGGVKRISGLI-amide (SEQ ID NO.:1).

Molecular Biology:

Full-length human PRMT1 isoform 1 (NM_(—)001536.5) transcript clone was amplified from an HEK 293 cDNA library, incorporating flanking 5′ sequence encoding a FLAG tag (DYKDDDDK) (SEQ ID NO.:2) fused directly to Met 1 of PRMT1. The amplified gene was subcloned into pFastBacI (Life Technologies) modified to encode an N-terminal GST tag and a TEV cleavage sequence

(SEQ ID NO.: 3) (MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELG LEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAV LDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVT HPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYI AWPLQGWQATFGGGDHPPKSDENLYFQGGNS) fused to Asp of the Flag tag of PRMT1.

Protein Expression.

Recombinant baculovirus were generated according to Bac-to-Bac kit instructions (Life Technologies). Protein over-expression was accomplished by infecting exponentially growing High Five insect cell culture at 1.5×10⁶ cell/ml with 1:100 ratio of virus. Infections were carried out at 27° C. for 48 hours, harvested by centrifugation, and stored at −80° C. for purification.

Protein Purification.

Expressed full-length human GST-tagged PRMT1 protein was purified from cell paste by glutathione sepharose affinity chromatography after equilibration of the resin with 50 mM phosphate buffer, 200 mM NaCl, 5% glycerol, 5 mM 3-mercaptoethanol, pH7.8 (Buffer A). GST-tagged PRMT1 was eluted with 50 mM Tris, 2 mM glutathione, pH 7.8, dialysed in buffer A and concentrated to 1 mg/mL. The purity of recovered protein was 73%. Reference: Wasilko, D. J. and S. E. Lee: “TIPS: titerless infected-cells preservation and scale-up” Bioprocess J., 5 (2006), pp. 29-32.

Predicted Translations:

GST-tagged PRMT1 (SEQ ID NO.: 4) MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGL EFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVL DIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTH PDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIA WPLQGWQATFGGGDHPPKSDENLYFQGGNSDYKDDDDKMAAAEAANCIME NFVATLANGMSLQPPLEEVSCGQAESSEKPNAEDMTSKDYYFDSYAHFGI HEEMLKDEVRTLTYRNSMFHNRHLFKDKVVLDVGSGTGILCMFAAKAGAR KVIGIECSSISDYAVKIVKANKLDHVVTIIKGKVEEVELPVEKVDIIISE WMGYCLFYESMLNTVLYARDKWLAPDGLIFPDRATLYVTAIEDRQYKDYK IHWWENVYGFDMSCIKDVAIKEPLVDVVDPKQLVTNACLIKEVDIYTVKV EDLTFTSPFCLQVKRNDYVHALVAYFNIEFTRCHKRTGFSTSPESPYTHW KQTVFYMEDYLTVKTGEEIFGTIGMRPNAKNNRDLDFTIDLDFKGQLCEL SCSTDYRMR

General Procedure for PRMT1 Enzyme Assays on Peptide Substrates.

The assays were all performed in a buffer consisting of 20 mM Bicine (pH=7.6), 1 mM TCEP, 0.005% BSG, and 0.002% Tween 20, prepared on the day of use. Compounds in 100% DMSO (1 ul) were spotted into a polypropylene 384-well V-bottom plates (Greiner) using a Platemate Plus outfitted with a 384-channel head (Thermo Scientific). DMSO (1 ul) was added to Columns 11, 12, 23, 24, rows A-H for the maximum signal control and 1 ul of SAH, a known product and inhibitor of PRMT1, was added to columns 11, 12, 23, 24, rows I-P for the minimum signal control. A cocktail (40 ul) containing the PRMT1 enzyme was added by Multidrop Combi (Thermo-Fisher). The compounds were allowed to incubate with PRMT1 for 30 min at room temperature, then a cocktail (10 ul) containing SAM and peptide was added to initiate the reaction (final volume=51 ul). The final concentrations of the components were as follows: PRMT1 was 0.5 nM, ³H-SAM was 200 nM, non-radiolabeled SAM was 1.5 uM, peptide was 20 nM, SAH in the minimum signal control wells was 1 mM, and the DMSO concentration was 2%. The assays were stopped by the addition of non-radiolabeled SAM (10 ul) to a final concentration of 300 uM, which dilutes the ³H-SAM to a level where its incorporation into the peptide substrate is no longer detectable. 50 ul of the reaction in the 384-well polypropylene plate was then transferred to a 384-well Flashplate and the biotinylated peptides were allowed to bind to the streptavidin surface for at least 1 hour before being washed once with 0.1% Tween20 in a Biotek EL×405 plate washer. The plates were then read in a PerkinElmer TopCount plate reader to measure the quantity of ³H-labeled peptide bound to the Flashplate surface, measured as disintegrations per minute (dpm) or alternatively, referred to as counts per minute (cpm).

%  inhibition  calculation ${\% \mspace{14mu} {inh}} = {100 - {\left( \frac{{dpm}_{cmpd} - {dpm}_{\min}}{{dpm}_{\max} - {dpm}_{\min}} \right) \times 100}}$

Where dpm=disintegrations per minute, cmpd=signal in assay well, and min and max are the respective minimum and maximum signal controls.

Four-parameter  IC 50  fit $Y = {{Bottom} + \frac{\left( {{Top} - {Bottom}} \right)}{\left( {1 + \left( \frac{X}{{IC}_{50}} \right)^{{Hill}\mspace{14mu} {Coefficient}}} \right.}}$

Where top and bottom are the normally allowed to float, but may be fixed at 100 or 0 respectively in a 3-parameter fit. The Hill Coefficient normally allowed to float but may also be fixed at 1 in a 3-parameter fit. Y is the % inhibition and X is the compound concentration.

PRMT6 Biochemical Assay

General Materials.

S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), bicine, Tween20, dimethylsulfoxide (DMSO), bovine skin gelatin (BSG), sodium butyrate and Tris(2-carboxyethyl)phosphine hydrochloride solution (TCEP) were purchased from Sigma-Aldrich at the highest level of purity possible. ³H-SAM was purchase from American Radiolabeled Chemicals with a specific activity of 80 Ci/mmol. 384-well streptavidin Flashplates were purchased from PerkinElmer.

Substrates.

Peptide representative of human histone H4 residues 36-50 was synthesized with an N-terminal linker-affinity tag motif and a C-terminal amide cap by 21^(st) Century Biochemicals. The peptide was purified by high-performance liquid chromatography (HPLC) to greater than 95% purity and confirmed by liquid chromatography mass spectrometry (LC-MS). The sequence was Biot-Ahx-RLARRGGVKRISGLI-amide and contained a monomethylated lysine at position 44 (SEQ ID NO.:5).

Molecular Biology:

Full-length human PRMT6 (NM_(—)018137.2) transcript clone was amplified from an HEK 293 cDNA library, incorporating a flanking 5′ sequence encoding a FLAG tag (MDYKDDDDK) (SEQ ID NO.:6) fused directly to Ser 2 of PRMT6 and a 3′ sequence encoding a hexa His sequence (HHHHHH) (SEQ ID NO.: 17) fused directly to Asp 375. The amplified gene was subcloned into pFastBacMam (Viva Biotech).

Protein Expression.

Recombinant baculovirus were generated according to Bac-to-Bac kit instructions (Life Technologies). Protein over-expression was accomplished by infecting exponentially growing HEK 293F cell culture at 1.3×10⁶ cell/ml with virus (MOI=10) in the presence of 8 mM sodium butyrate. Infections were carried out at 37° C. for 48 hours, harvested by centrifugation, and stored at −80° C. for purification.

Protein Purification.

Expressed full-length human Flag- and His-tagged PRMT6 protein was purified from cell paste by NiNTA agarose affinity chromatography after equilibration of the resin with buffer containing 50 mM Tris, 300 mM NaCl, 10% glycerol, pH 7.8 (Buffer Ni-A). Column was washed with 20 mM imidazole in the same buffer and Flag-PRMT6-His was eluted with 150 mM imidazole. Pooled fractions were dialysed against buffer Ni-A and further purified by anti-flag M2 affinity chromatography. Flag-PRMT6-His was eluted with 200 ug/ml FLAG peptide in the same buffer. Pooled fractions were dialysed in 20 mM Tris, 150 mM NaCl, 10% glycerol and 5 mM β-mercaptoethanol, pH 7.8. The purity of recovered protein was 95%.

Predicted Translations:

Flag-PRMT6-His (SEQ ID NO.: 7) MDYKDDDDKSQPKKRKLESGGGGEGGEGTEEEDGAEREAALERPRRTKRE RDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVLDVGAG TGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPGPVET VELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASAELF IAPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIVVQGLS GEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPMHGFAIWF QVTFPGGESEKPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVSGEIT LLPSRDNPRRLRVLLRYKVGDQEEKTKDFAMEDHHHHHH

General Procedure for PRMT6 Enzyme Assays on Peptide Substrates.

The assays were all performed in a buffer consisting of 20 mM Bicine (pH=7.6), 1 mM TCEP, 0.005% BSG, and 0.002% Tween 20, prepared on the day of use. Compounds in 100% DMSO (1 ul) were spotted into a polypropylene 384-well V-bottom plates (Greiner) using a Platemate Plus outfitted with a 384-channel head (Thermo Scientific). DMSO (1 ul) was added to Columns 11, 12, 23, 24, rows A-H for the maximum signal control and 1 ul of SAH, a known product and inhibitor of PRMT6, was added to columns 11, 12, 23, 24, rows I-P for the minimum signal control. A cocktail (40 ul) containing the PRMT6 enzyme was added by Multidrop Combi (Thermo-Fisher). The compounds were allowed to incubate with PRMT6 for 30 min at room temperature, then a cocktail (10 ul) containing SAM and peptide was added to initiate the reaction (final volume=51 ul). The final concentrations of the components were as follows: PRMT6 was 1 nM, ³H-SAM was 200 nM, non-radiolabeled SAM was 250 nM, peptide was 75 nM, SAH in the minimum signal control wells was 1 mM, and the DMSO concentration was 2%. The assays were stopped by the addition of non-radiolabeled SAM (10 ul) to a final concentration of 400 uM, which dilutes the ³H-SAM to a level where its incorporation into the peptide substrate is no longer detectable. 50 ul of the reaction in the 384-well polypropylene plate was then transferred to a 384-well Flashplate and the biotinylated peptides were allowed to bind to the streptavidin surface for at least 1 hour before being washed once with 0.1% Tween20 in a Biotek EL×405 plate washer. The plates were then read in a PerkinElmer TopCount plate reader to measure the quantity of ³H-labeled peptide bound to the Flashplate surface, measured as disintegrations per minute (dpm) or alternatively, referred to as counts per minute (cpm).

%  inhibition  calculation ${\% \mspace{14mu} {inh}} = {100 - {\left( \frac{{dpm}_{cmpd} - {dpm}_{\min}}{{dpm}_{\max} - {dpm}_{\min}} \right) \times 100}}$

Where dpm=disintegrations per minute, cmpd=signal in assay well, and min and max are the respective minimum and maximum signal controls.

Four-parameter  IC 50  fit $Y = {{Bottom} + \frac{\left( {{Top} - {Bottom}} \right)}{\left( {1 + \left( \frac{X}{{IC}_{50}} \right)^{{Hill}\mspace{14mu} {Coefficient}}} \right.}}$

Where top and bottom are the normally allowed to float, but may be fixed at 100 or 0 respectively in a 3-parameter fit. The Hill Coefficient normally allowed to float but may also be fixed at 1 in a 3-parameter fit. Y is the % inhibition and X is the compound concentration.

PRMT8 Biochemical Assay

General Materials.

S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), bicine, Tween20, dimethylsulfoxide (DMSO), bovine skin gelatin (BSG), isopropyl-β-D-thiogalactopyranoside (IPTG), and Tris(2-carboxyethyl)phosphine hydrochloride solution (TCEP) were purchased from Sigma-Aldrich at the highest level of purity possible. ³H-SAM was purchase from American Radiolabeled Chemicals with a specific activity of 80 Ci/mmol. 384-well streptavidin Flashplates were purchased from PerkinElmer.

Substrates.

Peptide representative of human histone H4 residues 31-45 was synthesized with an N-terminal linker-affinity tag motif and a C-terminal amide cap by 21^(st) Century Biochemicals. The peptide was purified by high-performance liquid chromatography (HPLC) to greater than 95% purity and confirmed by liquid chromatography mass spectrometry (LC-MS). The sequence was Biot-Ahx-KPAIRRLARRGGVKR-amide (SEQ ID NO.:8).

Molecular Biology:

Full-length human PRMT8 (NM_(—)019854.4) isoform 1 transcript clone was amplified from an HEK 293 cDNA library and subcloned into pGEX-4T-1 (GE Life Sciences). The resulting construct encodes an N-terminal GST tag and a thrombin cleavage sequence

(SEQ ID NO.: 9) (MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELG LEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAV LDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVT HPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYI AWPLQGWQATFGGGDHPPKSDLVPRGSPEF) fused directly to Met 1 of PRMT8.

Protein Expression.

E. coli (BL21(DE3) Gold, Stratagene) made competent by the CaCl₂ method were transformed with the PRMT8 construct and ampicillin selection. Protein over-expression was accomplished by growing the PRMT8 expressing E. coli clone and inducing expression with 0.3 mM IPTG at 16° C. The culture was grown for 12 hours, harvested by centrifugation, and stored at −80° C. for purification.

Protein Purification.

Expressed full-length human GST-tagged PRMT8 protein was purified from cell paste by glutathione sepharose affinity chromatography after the resin was equilibrated with 50 mM phosphate buffer, 200 mM NaCl, 5% glycerol, 5 mM β-mercaptoethanol, pH7.8 (Buffer A). GST-tagged PRMT8 was eluted with 50 mM Tris, 2 mM glutathione, pH 7.8. Pooled fractions were cleaved by thrombin (10 U) and dialysed in buffer A. GST was removed by reloading the cleaved protein sample onto glutathione sepharose column and PRMT8 was collected in the flow-through fractions. PRMT8 was purified further by ceramic hydroxyapatite chromatography. The column was washed with 50 mM phosphate buffer, 100 mM NaCl, 5% glycerol, 5 mM (3-mercaptoethanol, pH 7.8 and PRMT8 was eluted by 100 mM phosphate in the same buffer. Protein was concentrated and buffer was exchanged to 50 mM Tris, 300 mM NaCl, 10% glycerol, 5 mM β-mercaptoethanol, pH 7.8 by ultrafiltration. The purity of recovered protein was 89%.

Predicted Translations:

GST-tagged PRMT8 (SEQ ID NO.: 10) MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGL EFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVL DIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTH PDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIA WPLQGWQATFGGGDHPPKSDLVPRGSPEFMGMKHSSRCLLLRRKMAENAA ESTEVNSPPSQPPQPVVPAKPVQCVHHVSTQPSCPGRGKMSKLLNPEEMT SRDYYFDSYAHFGIHEEMLKDEVRTLTYRNSMYHNKHVFKDKVVLDVGSG TGILSMFAAKAGAKKVFGIECSSISDYSEKIIKANHLDNIITIFKGKVEE VELPVEKVDIIISEWMGYCLFYESMLNTVIFARDKWLKPGGLMFPDRAAL YVVAIEDRQYKDFKIHWWENVYGFDMTCIRDVAMKEPLVDIVDPKQVVTN ACLIKEVDIYTVKTEELSFTSAFCLQIQRNDYVHALVTYFNIEFTKCHKK MGFSTAPDAPYTHWKQTVFYLEDYLTVRRGEEIYGTISMKPNAKNVRDLD FTVDLDFKGQLCETSVSNDYKMR

General Procedure for PRMT8 Enzyme Assays on Peptide Substrates.

The assays were all performed in a buffer consisting of 20 mM Bicine (pH=7.6), 1 mM TCEP, 0.005% BSG, and 0.002% Tween 20, prepared on the day of use. Compounds in 100% DMSO (1 ul) were spotted into a polypropylene 384-well V-bottom plates (Greiner) using a Platemate Plus outfitted with a 384-channel head (Thermo Scientific). DMSO (1 ul) was added to Columns 11, 12, 23, 24, rows A-H for the maximum signal control and 1 ul of SAH, a known product and inhibitor of PRMT8, was added to columns 11, 12, 23, 24, rows I-P for the minimum signal control. A cocktail (40 ul) containing the PRMT8 enzyme was added by Multidrop Combi (Thermo-Fisher). The compounds were allowed to incubate with PRMT8 for 30 min at room temperature, then a cocktail (10 ul) containing ³H-SAM and peptide was added to initiate the reaction (final volume=51 ul). The final concentrations of the components were as follows: PRMT8 was 1.5 nM, ³H-SAM was 50 nM, non-radiolabeled SAM was 550 nM, peptide was 150 nM, SAH in the minimum signal control wells was 1 mM, and the DMSO concentration was 2%. The assays were stopped by the addition of non-radiolabeled SAM (10 ul) to a final concentration of 400 uM, which dilutes the ³H-SAM to a level where its incorporation into the peptide substrate is no longer detectable. 50 ul of the reaction in the 384-well polypropylene plate was then transferred to a 384-well Flashplate and the biotinylated peptides were allowed to bind to the streptavidin surface for at least 1 hour before being washed once with 0.1% Tween20 in a Biotek EL×405 plate washer. The plates were then read in a PerkinElmer TopCount plate reader to measure the quantity of ³H-labeled peptide bound to the Flashplate surface, measured as disintegrations per minute (dpm) or alternatively, referred to as counts per minute (cpm).

%  inhibition  calculation ${\% \mspace{14mu} {inh}} = {100 - {\left( \frac{{dpm}_{cmpd} - {dpm}_{\min}}{{dpm}_{\max} - {dpm}_{\min}} \right) \times 100}}$

Where dpm=disintegrations per minute, cmpd=signal in assay well, and min and max are the respective minimum and maximum signal controls.

Four-parameter  IC 50  fit $Y = {{Bottom} + \frac{\left( {{Top} - {Bottom}} \right)}{\left( {1 + \left( \frac{X}{{IC}_{50}} \right)^{{Hill}\mspace{14mu} {Coefficient}}} \right.}}$

Where top and bottom are the normally allowed to float, but may be fixed at 100 or 0 respectively in a 3-parameter fit. The Hill Coefficient normally allowed to float but may also be fixed at 1 in a 3-parameter fit. Y is the % inhibition and X is the compound concentration.

PRMT3 Biochemical Assay

General Materials.

S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), bicine, Tween20, dimethylsulfoxide (DMSO), bovine skin gelatin (BSG), isopropyl-β-D-thiogalactopyranoside (IPTG), and Tris(2-carboxyethyl)phosphine hydrochloride solution (TCEP) were purchased from Sigma-Aldrich at the highest level of purity possible. ³H-SAM was purchase from American Radiolabeled Chemicals with a specific activity of 80 Ci/mmol. 384-well streptavidin Flashplates were purchased from PerkinElmer.

Substrates.

Peptide containing the classic RMT substrate motif was synthesized with an N-terminal linker-affinity tag motif and a C-terminal amide cap by 21^(st) Century Biochemicals. The peptide was purified by high-performance liquid chromatography (HPLC) to greater than 95% purity and confirmed by liquid chromatography mass spectrometry (LC-MS). The sequence was Biot-Ahx-GGRGGFGGRGGFGGRGGFG-amide (SEQ ID NO.:11).

Molecular Biology:

Full-length human PRMT3 (NM_(—)005788.3) isoform 1 transcript clone was amplified from an HEK 293 cDNA library and subcloned into pGEX-KG (GE Life Sciences). The resulting construct encodes an N-terminal GST tag and a thrombin cleavage sequence

(SEQ ID NO.: 12) (MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELG LEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAV LDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVT HPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYI AWPLQGWQATFGGGDHPPKSDLVPRGS) fused directly to Cys 2 of PRMT3.

Protein Expression.

E. coli (BL21(DE3) Gold, Stratagene) made competent by the CaCl₂ method were transformed with the PRMT3 construct and ampicillin selection. Protein over-expression was accomplished by growing the PRMT3 expressing E. coli clone and inducing expression with 0.3 mM IPTG at 16° C. The culture was grown for 12 hours, harvested by centrifugation, and stored at −80° C. for purification.

Protein Purification.

Expressed full-length human GST-tagged PRMT3 protein was purified from cell paste by glutathione sepharose affinity chromatography after equilibration of the resin with 50 mM phosphate buffer, 200 mM NaCl, 5% glycerol, 1 mM EDTA, 5 mM β-mercaptoethanol, pH6.5 (Buffer A). GST-tagged PRMT3 was eluted with 50 mM Tris, 2 mM glutathione, pH 7.1 and 50 mM Tris, 20 mM glutathione, pH 7.1. Pooled fractions were dialysed in 20 mM Tris, 50 mM NaCl, 5% glycerol, 1 mM EDTA, 1 mM DTT, pH7.5 (Buffer B) and applied to a Q Sepharose Fast Flow column. GST-tagged PRMT3 was eluted by 500 mM NaCl in buffer B. Pooled fractions were dialyzed in 25 mM phosphate buffer, 100 mM NaCl, 5% glycerol, 2 mM DTT, pH 6.8 (Buffer C) and loaded on to a ceramic hydroxyapatite column. GST-tagged PRMT3 eluted with 25-400 mM phosphate in buffer C. Protein was concentrated and buffer was exchanged to 20 mM Tris, 150 mM NaCl, 5% glycerol, 5 mM β-mercaptoethanol, pH7.8 by ultrafiltration. The purity of recovered protein was 70%.

Predicted Translations:

GST-tagged PRMT3 (SEQ ID NO.: 13) MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGL EFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVL DIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTH PDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIA WPLQGWQATFGGGDHPPKSDLVPRGSCSLASGATGGRGAVENEEDLPELS DSGDEAAWEDEDDADLPHGKQQTPCLFCNRLFTSAEETFSHCKSEHQFNI DSMVHKHGLEFYGYIKLINFIRLKNPTVEYMNSIYNPVPWEKEEYLKPVL EDDLLLQFDVEDLYEPVSVPFSYPNGLSENTSVVEKLKHMEARALSAEAA LARAREDLQKMKQFAQDFVMHTDVRTCSSSTSVIADLQEDEDGVYFSSYG HYGIHEEMLKDKIRTESYRDFIYQNPHIFKDKVVLDVGCGTGILSMFAAK AGAKKVLGVDQSEILYQAMDIIRLNKLEDTITLIKGKIEEVHLPVEKVDV IISEWMGYFLLFESMLDSVLYAKNKYLAKGGSVYPDICTISLVAVSDVNK HADRIAFWDDVYGFKMSCMKKAVIPEAVVEVLDPKTLISEPCGIKHIDCH TTSISDLEFSSDFTLKITRTSMCTAIAGYFDIYFEKNCHNRVVFSTGPQS TKTHWKQTVFLLEKPFSVKAGEALKGKVTVHKNKKDPRSLTVTLTLNNST QTYGLQ

General Procedure for PRMT3 Enzyme Assays on Peptide Substrates.

The assays were all performed in a buffer consisting of 20 mM Bicine (pH=7.6), 1 mM TCEP, 0.005% BSG, and 0.002% Tween 20, prepared on the day of use. Compounds in 100% DMSO (1 ul) were spotted into a polypropylene 384-well V-bottom plates (Greiner) using a Platemate Plus outfitted with a 384-channel head (Thermo Scientific). DMSO (1 ul) was added to Columns 11, 12, 23, 24, rows A-H for the maximum signal control and 1 ul of SAH, a known product and inhibitor of PRMT3, was added to columns 11, 12, 23, 24, rows I-P for the minimum signal control. A cocktail (40 ul) containing the PRMT3 enzyme was added by Multidrop Combi (Thermo-Fisher). The compounds were allowed to incubate with PRMT3 for 30 min at room temperature, then a cocktail (10 ul) containing SAM and peptide was added to initiate the reaction (final volume=51 ul). The final concentrations of the components were as follows: PRMT3 was 0.5 nM, ³H-SAM was 100 nM, non-radiolabeled SAM was 1.8 uM, peptide was 330 nM, SAH in the minimum signal control wells was 1 mM, and the DMSO concentration was 2%. The assays were stopped by the addition of potassium chloride (10 ul) to a final concentration of 100 mM. 50 ul of the reaction in the 384-well polypropylene plate was then transferred to a 384-well Flashplate and the biotinylated peptides were allowed to bind to the streptavidin surface for at least 1 hour before being washed once with 0.1% Tween20 in a Biotek EL×405 plate washer. The plates were then read in a PerkinElmer TopCount plate reader to measure the quantity of ³H-labeled peptide bound to the Flashplate surface, measured as disintegrations per minute (dpm) or alternatively, referred to as counts per minute (cpm).

%  inhibition  calculation ${\% \mspace{14mu} {inh}} = {100 - {\left( \frac{{dpm}_{cmpd} - {dpm}_{\min}}{{dpm}_{\max} - {dpm}_{\min}} \right) \times 100}}$

Where dpm=disintegrations per minute, cmpd=signal in assay well, and min and max are the respective minimum and maximum signal controls.

Four-parameter  IC 50  fit $Y = {{Bottom} + \frac{\left( {{Top} - {Bottom}} \right)}{\left( {1 + \left( \frac{X}{{IC}_{50}} \right)^{{Hill}\mspace{14mu} {Coefficient}}} \right.}}$

Where top and bottom are the normally allowed to float, but may be fixed at 100 or 0 respectively in a 3-parameter fit. The Hill Coefficient normally allowed to float but may also be fixed at 1 in a 3-parameter fit. Y is the % inhibition and X is the compound concentration.

CARM1 Biochemical Assay

General Materials.

S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), bicine, Tween20, dimethylsulfoxide (DMSO), bovine skin gelatin (BSG), sodium butyrate and Tris(2-carboxyethyl)phosphine hydrochloride solution (TCEP) were purchased from Sigma-Aldrich at the highest level of purity possible. ³H-SAM was purchase from American Radiolabeled Chemicals with a specific activity of 80 Ci/mmol. 384-well streptavidin Flashplates were purchased from PerkinElmer.

Substrates.

Peptide representative of human histone H3 residues 16-30 was synthesized with an N-terminal linker-affinity tag motif and a C-terminal amide cap by 21^(st) Century Biochemicals. The peptide was purified by high-performance liquid chromatography (HPLC) to greater than 95% purity and confirmed by liquid chromatography mass spectrometry (LC-MS). The sequence was Biot-Ahx-PRKQLATKAARKSAP-amide and contained a monomethylated arginine at position 26 (SEQ ID NO.: 14).

Molecular Biology:

Human CARM1 (PRMT4) (NM_(—)199141.1) transcript clone was amplified from an HEK 293 cDNA library, incorporating a flanking 5′ sequence encoding a FLAG tag (MDYKDDDDK) (SEQ ID NO.:6) fused directly to Ala 2 of CARM1 and 3′ sequence encoding a hexa His sequence (EGHHHHHH) (SEQ ID NO.: 15) fused directly to Ser 608. The gene sequence encoding isoform1 containing a deletion of amino acids 539-561 was amplified subsequently and subcloned into pFastBacMam (Viva Biotech).

Protein Expression.

Recombinant baculovirus were generated according to Bac-to-Bac kit instructions (Life Technologies). Protein over-expression was accomplished by infecting exponentially growing HEK 293F cell culture at 1.3×10⁶ cell/ml with virus (MOI=10) in the presence of 8 mM sodium butyrate. Infections were carried out at 37° C. for 48 hours, harvested by centrifugation, and stored at −80° C. for purification.

Protein Purification.

Expressed full-length human Flag- and His-tagged CARM1 protein was purified from cell paste by anti-flag M2 affinity chromatography with resin equilibrated with buffer containing 20 mM Tris, 150 mM NaCl, 5% glycerol, pH 7.8. Column was washed with 500 mM NaCl in buffer A and Flag-CARM1-His was eluted with 200 ug/ml FLAG peptide in buffer A. Pooled fractions were dialyzed in 20 mM Tris, 150 mM NaCl, 5% glycerol and 1 mM DTT, pH 7.8. The purity of recovered protein was 94.

Predicted Translations:

Flag-CARM1-His (SEQ ID NO.: 16) MDYKDDDDKAAAAAAVGPGAGGAGSAVPGGAGPCATVSVFPGARLLTIGD ANGEIQRHAEQQALRLEVRAGPDSAGIALYSHEDVCVFKCSVSRETECSR VGKQSFIITLGCNSVLIQFATPNDFCSFYNILKTCRGHTLERSVFSERTE ESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVG CGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKV EEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDV HLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDT FDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFD VAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIA NKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTTPSPPPGSHYTSP SENMWNTGSTYNLSSGMAVAGMPTAYDLSSVIASGSSVGHNNLIPLGSSG AQGSGGGSTSAHYAVNSQFTMGGPAISMASPMSIPTNTMHYGSEGHHHHH H

General Procedure for CARM1 Enzyme Assays on Peptide Substrates.

The assays were all performed in a buffer consisting of 20 mM Bicine (pH=7.6), 1 mM TCEP, 0.005% BSG, and 0.002% Tween 20, prepared on the day of use. Compounds in 100% DMSO (1 ul) were spotted into a polypropylene 384-well V-bottom plates (Greiner) using a Platemate Plus outfitted with a 384-channel head (Thermo Scientific). DMSO (1 ul) was added to Columns 11, 12, 23, 24, rows A-H for the maximum signal control and 1 ul of SAH, a known product and inhibitor of CARM1, was added to columns 11, 12, 23, 24, rows I-P for the minimum signal control. A cocktail (40 ul) containing the CARM1 enzyme was added by Multidrop Combi (Thermo-Fisher). The compounds were allowed to incubate with CARM1 for 30 min at room temperature, then a cocktail (10 ul) containing ³H-SAM and peptide was added to initiate the reaction (final volume=51 ul). The final concentrations of the components were as follows: CARM1 was 0.25 nM, ³H-SAM was 30 nM, peptide was 250 nM, SAH in the minimum signal control wells was 1 mM, and the DMSO concentration was 2%. The assays were stopped by the addition of non-radiolabeled SAM (10 ul) to a final concentration of 300 uM, which dilutes the ³H-SAM to a level where its incorporation into the peptide substrate is no longer detectable. 50 ul of the reaction in the 384-well polypropylene plate was then transferred to a 384-well Flashplate and the biotinylated peptides were allowed to bind to the streptavidin surface for at least 1 hour before being washed once with 0.1% Tween20 in a Biotek EL×405 plate washer. The plates were then read in a PerkinElmer TopCount plate reader to measure the quantity of ³H-labeled peptide bound to the Flashplate surface, measured as disintegrations per minute (dpm) or alternatively, referred to as counts per minute (cpm).

%  inhibition  calculation ${\% \mspace{14mu} {inh}} = {100 - {\left( \frac{{dpm}_{cmpd} - {dpm}_{\min}}{{dpm}_{\max} - {dpm}_{\min}} \right) \times 100}}$

Where dpm=disintegrations per minute, cmpd=signal in assay well, and min and max are the respective minimum and maximum signal controls.

Four-parameter  IC 50  fit $Y = {{Bottom} + \frac{\left( {{Top} - {Bottom}} \right)}{\left( {1 + \left( \frac{X}{{IC}_{50}} \right)^{{Hill}\mspace{14mu} {Coefficient}}} \right.}}$

Where top and bottom are the normally allowed to float, but may be fixed at 100 or 0 respectively in a 3-parameter fit. The Hill Coefficient normally allowed to float but may also be fixed at 1 in a 3-parameter fit. Y is the % inhibition and X is the compound concentration.

The biochemical evaluation of the exemplary compounds are shown in Tables 2 and 2a.

TABLE 2 Biochemical evaluation Cmpd No. PRMT1 PRMT6 PRMT8 PRMT3 PRMT4  1B A A B — —  2 A B B — —  3 A B — — —  4 A A — — —  5 A A — — —  6 A A — — —  7 A A — — —  8 A A — — —  9 A A — — — 10 A B — — — 11 A A — — — 12 A A — — — 13 A A — — — 14 A A — — — 17 A A — — — 18 A A — — B 19 A A A — — 20 A A A — — 21 A A A — — 22 A A — — B 23 A A — — B 24 A B — — A 25 A A — — B 26 A B — — B 27 A B — — B 28 A B — — C 29 A B — — B 30 A B — — B 31 A C B — — 32 B A — — B 33 B A C — — 34 D D — — D 35 D D — — D 36 B C — — D 37 C B — — C 38 D B — — C 39 A B — — B 40 B C C — D 41 B C C — C 42 A A B — C 43 A A B — B 44 A A A — B 45 A A A — B 46 A A A — B 47 A A A — B 48 A A A — B 49 D D — — D 50 D D — — D 51 C C — — D 52 C C — — D 53 D C — — D 54 B B — — D 55 A B — — B 56 A B — — B 57 B B — — B 58 B B — — C 59 A B — — A 60 A B — — B 61 A B — — D 62 C B — — C 63 B B — — D 64 A A — — C 65 A A — — B 66 A A — — C 67 A A — — D 68 B A — — D 69 B A — — D 70 B A — — B 71 B A — — D 72 A A — — B 73 A A — — B 74 B A — — B For Table 2, “A” indicates an IC₅₀ ≦ 0.100 μM, “B” indicates an IC₅₀ of 0.101-1.00 μM, “C” indicates an IC₅₀ of 1.01-3.00 μM, “D” indicates an IC₅₀ of 3.01-10 μM, and IC₅₀ ≧ 10.01 μM.

TABLE 2a Biochemical evaluation (Numerical, μM)* Cmpd No. PRMT1 PRMT6 PRMT8 PRMT3 PRMT4  1B 0.00359 0.00944 0.26738 — —  2 0.02101 0.11347 0.45753 — —  3 0.05623 0.51374 — — —  4 0.00681 0.0364 — — —  5 0.03852 0.08485 — — —  6 0.01898 0.0393 — — —  7 0.0066 0.00678 — — —  8 0.00783 0.05604 — — —  9 0.01083 0.01385 — — — 10 0.01617 0.12465 — — — 11 0.0033 0.00968 — — — 12 0.02724 0.04413 — — — 13 0.08687 0.00447 — — — 14 0.02328 0.00529 — — — 17 0.05175 0.00781 — — — 18 0.04023 0.01028 — — — 19 0.0159 0.0193 — — — 20 0.00633 0.03735 — — 0.15262 21 0.01314 0.02152 0.06746 — — 22 0.01192 0.03313 0.08016 — — 23 0.01199 0.09658 0.04279 — — 24 0.01271 0.08033 — — 0.11495 25 0.08189 0.00505 — — 0.93158 26 0.04396 0.2014 — — 0.03509 27 0.03157 0.05369 — — 0.38998 28 0.02247 0.15013 — — 0.26019 29 0.02824 0.17781 — — 0.44623 30 0.06447 0.13069 — — 2.33513 31 0.04654 0.13455 — — 0.42264 32 0.0739 0.15641 — — 0.18809 33 0.04449 1.10777 0.27307 — — 34 0.18246 0.0149 — — 0.31014 35 0.18715 0.03565 1.85787 — — 36 6.76277 6.67208 — — 6.13172 37 6.41731 4.84196 — — >10 38 0.55158 1.87148 — — >10 39 2.27415 0.69353 — — 2.87839 40 3.90733 0.22285 — — 2.10638 41 0.06762 0.14475 — — 0.23992 42 0.77433 2.33758 2.85312 — 4.04533 43 0.43424 1.80476 2.00147 — 1.7843 44 0.04361 0.07196 0.23585 — 1.01309 45 0.03744 0.05813 0.13342 — 0.16009 46 0.02122 0.04058 0.09883 — 0.25949 47 0.05555 0.07429 0.09179 — 0.37036 48 0.03403 0.06556 0.08345 — 0.44035 49 0.01574 0.05189 0.04539 — 0.60551 50 0.01095 0.04497 0.03868 — 0.24521 51 5.52412 >10 — — >10 52 3.6919 6.02257 — — >10 53 1.7608 2.5526 — — >10 54 2.00476 2.32997 — — >10 55 6.54741 1.01577 — — >10 56 0.99432 0.77415 — — >10 57 0.04327 0.47865 — — 0.33324 58 0.0579 0.44711 — — 0.24801 59 0.10071 0.30555 — — 0.31342 60 0.35312 0.24307 — — 1.76615 61 0.04079 0.23565 — — 0.08728 62 0.0565 0.19144 — — 0.36363 63 0.09862 0.16356 — — 4.15643 64 2.63175 0.10723 — — 1.96077 65 0.12829 0.10467 — — 4.94407 66 0.03498 0.05638 — — 1.90811 67 0.02477 0.05616 — — 0.68289 68 0.09153 0.03967 — — 1.69834 69 0.03027 0.03424 — — 4.16351 70 0.18754 0.01515 — — 3.69918 71 0.20335 0.01309 — — 3.79024 72 0.18224 0.01266 — — 0.8917 73 0.14272 0.00949 — — 4.59231 74 0.02298 0.00909 — — 0.30469 *For Table 2a, numerical values represent data from a single experiment or an average of multiple experiments.

RKO Methylation Assay

RKO adherent cells were purchased from ATCC (American Type Culture Collection), Manassas, Va., USA. DMEM/Glutamax medium, penicillin-streptomycin, heat inactivated fetal bovine serum, 0.05% trypsin and D-PBS were purchased from Life Technologies, Grand Island, N.Y., USA. Odyssey blocking buffer, 800CW goat anti-rabbit IgG (H+L) antibody, and Licor Odyssey infrared scanner were purchased from Licor Biosciences, Lincoln, Nebr., USA. Mono-methyl arginine antibody was purchased from Cell Signaling Technology, Danvers, Mass., USA. Methanol was purchased from VWR, Franklin, Mass., USA. 10% Tween 20 was purchased from KPL, Inc., Gaithersburg, Md., USA. DRAQ5 was purchased from Biostatus Limited, Leicestershire, UK.

RKO adherent cells were maintained in growth medium (DMEM/Glutamax medium supplemented with 10% v/v heat inactivated fetal bovine serum and 100 units/mL penicillin-streptomycin) and cultured at 37° C. under 5% CO₂.

Cell Treatment, in Cell Western (ICW) for Detection of Mono-Methyl Arginine and DNA Content.

RKO cells were seeded in assay medium at a concentration of 20,000 cells per mL to a poly-D-lysine coated 384 well culture plate (BD Biosciences 356697) with 50 μL per well. Compound (100 nL) from a 96-well source plate was added directly to 384 well cell plate. Plates were incubated at 37° C., 5% CO₂ for 72 hours. After three days of incubation, plates were brought to room temperature outside of the incubator for ten minutes and blotted on paper towels to remove cell media. 50 μL of ice cold 100% methanol was added directly to each well and incubated for 30 min at room temperature. After 30 min, plates were transferred to a Biotek EL406 plate washer and washed 2 times with 100 μL per well of wash buffer (1×PBS). Next 60 μL per well of Odyssey blocking buffer (Odyssey Buffer with 0.1% Tween 20 (v/v)) were added to each plate and incubated 1 hour at room temperature. Blocking buffer was removed and 20 μL per well of primary antibody was added (mono-methyl arginine diluted 1:200 in Odyssey buffer with 0.1% Tween 20 (v/v)) and plates were incubated overnight (16 hours) at 4° C. Plates were washed 5 times with 100 μL per well of wash buffer. Next 20 μL per well of secondary antibody was added (1:200 800CW goat anti-rabbit IgG (H+L) antibody, 1:1000 DRAQ5 (Biostatus limited) in Odyssey buffer with 0.1% Tween 20 (v/v)) and incubated for 1 hour at room temperature. The plates were washed 5 times with 100 μL per well wash buffer then 2 times with 100 μL per well of water. Plates were allowed to dry at room temperature then imaged on the Licor Odyssey machine which measures integrated intensity at 700 nm and 800 nm wavelengths. Both 700 and 800 channels were scanned.

Calculations:

First, the ratio for each well was determined by:

$\left( \frac{{monomethyl}\mspace{14mu} {Arginine}\mspace{14mu} 800\mspace{14mu} {nm}\mspace{14mu} {value}}{{DRAQ}\; 5\mspace{14mu} 700\mspace{14mu} {nm}\mspace{14mu} {value}} \right)$

Each plate included fourteen control wells of DMSO only treatment (minimum activation) as well as fourteen control wells for maximum activation treated with 20 μM of a reference compound. The average of the ratio values for each control type was calculated and used to determine the percent activation for each test well in the plate. Reference compound was serially diluted three-fold in DMSO for a total of nine test concentrations, beginning at 20 μM. Percent activation was determined and EC₃₀ curves were generated using triplicate

${{Percent}\mspace{14mu} {Activation}} = {100 - \left( {\left( \frac{\left( {{Individual}\mspace{14mu} {Test}{\mspace{11mu} \;}{Sample}\mspace{14mu} {Ratio}} \right) - \left( {{Minimum}\mspace{14mu} {Activation}\mspace{14mu} {Ratio}} \right)}{\left( {{Maximum}\mspace{14mu} {Activation}\mspace{14mu} {Ratio}} \right) - \left( {{Minimum}{\mspace{11mu} \;}{Activation}\mspace{14mu} {Ratio}} \right)} \right)*100} \right)}$

TABLE 3 In Cell Western Data Cmpd No. RGG ICW EC30  1B A  2 B  3 C  4 A  5 B  6 A  7 A  8 A  9 B 10 B 11 A 12 B 13 B 14 B 17 C 18 A 19 A 20 A 21 A 22 A 23 A 24 A 25 A 26 B 27 B 28 B 29 B 30 B 31 B 32 B 33 B 34 C 35 C 36 C 37 C 38 C 39 C 40 — 41 — 42 — 43 — 44 — 45 — 46 — 47 — 48 — 49 — 50 — 51 — 52 — 53 — 54 — 55 — 56 — 57 — 58 — 59 — 60 — 61 — 62 — 63 — 64 — 65 — 66 — 67 — 68 — 69 — 70 — 71 — 72 — 73 — 74 — For Table 3, “A” indicates an EC₃₀ ≦3.00 μM, “B” indicates an EC₃₀ of 3.01-12.00 μM, and “C” indicates an EC₃₀ ≧12.01 μM.

TABLE 3a In Cell Western Data (Numerical, μM)* Cmpd No RGG ICW  1B 1.714  2 4.211  3 14.037  4 1.684  5 11.36  6 1.552  7 0.791  8 0.93  9 3.429 10 3.83 11 0.724 12 6.056 13 3.815 14 4.136 17 8.991 18 0.582 19 0.68 20 0.71 21 0.912 22 1.494 23 1.762 24 1.927 25 2.66 26 3.067 27 4.472 28 4.617 29 5.035 30 7.196 31 8.236 32 8.904 33 9.063 34 >20 35 >20 36 >20 37 >20 38 >20 39 >20 40 — 41 — 42 — 43 — 44 — 45 — 46 — 47 — 48 — 49 — 50 — 51 — 52 — 53 — 54 — 55 — 56 — 57 — 58 — 59 — 60 — 61 — 62 — 63 — 64 — 65 — 66 — 67 — 68 — 69 — 70 — 71 — 72 — 73 — 74 — *For Table 3a, numerical values represent data from a single experiment or an average of multiple experiments.

Other Embodiments

The foregoing has been a description of certain non-limiting embodiments of the invention. Those of ordinary skill in the art will appreciate that various changes and modifications to this description may be made without departing from the spirit or scope of the present invention, as defined in the following claims. 

What is claimed is:
 1. A compound of Formula (I):

or a pharmaceutically acceptable salt thereof, wherein: X is NR₂ and Y is N; or X is N and Y is NR₂; each instance of R₁ is independently selected from the group consisting of hydrogen, halogen, —N₃, —CN, —NO₂, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, —OR^(A), —N(R^(B))₂, —SR^(A), —C(═O)R^(A), —C(═O)OR^(A), —C(═O)SR^(A), —C(═O)N(R^(B))₂, —C(═O)N(R^(B))N(R^(B))₂, —OC(═O)R^(A), —OC(═O)N(R^(B))₂, —NR^(B)C(═O)R^(A), —NR^(B)C(═O)N(R^(B))₂, —NR^(B)C(═O)N(R^(B))N(R^(B))₂, —NR^(B)C(═O)OR^(A), —SC(═O)R^(A), —C(═NR^(B))R^(A), —C(═NNR^(B))R^(A), —C(═NOR^(A))R^(A), —C(═NR^(B))N(R^(B))₂, —NR^(B)C(═NR^(B))R^(B), —C(═S)R^(A), —C(═S)N(R^(B))₂, —NR^(B)C(═S)R^(A), —S(═O)R^(A), —OS(═O)₂R^(A), —SO₂R^(A), —NR^(B)SO₂R^(A), —SO₂N(R^(B))₂, or —Z—R₄; Z is a bond, —O—, —S—, —NR^(B)—, —NR^(B)C(═O)—, —C(═O)NR^(B)—, —OC(═O)NR^(B)—, —NR^(B)C(═O)O—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, trans-CR^(C)═CR^(C)—, cis-CR^(C)═CR^(C)—, —C≡C—, —OC(R^(C))₂—, —C(R^(C))₂O—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(B)—, —NR^(B)S(═O)₂—, or an optionally substituted C₁₋₈ hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NR^(B)—, —NR^(B)C(═O)—, —C(═O)NR^(B)—, —OC(═O)NR^(B)—, —NR^(B)C(═O)O—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(B)C(═S)—, —C(═S)NR^(B)—, trans-CR^(C)═CR^(C)—, cis-CR^(C)═CR^(C)—, —C≡C—, —OC(R^(C))₂—, —C(R^(C))₂O—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(B)—, —NR^(B)S(═O)₂—, wherein each instance of R^(C) is independently selected from the group consisting of hydrogen, halogen optionally substituted alkyl, optionally substituted alkenyl, optionally substituted carbocyclyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted heterocyclyl, and optionally substituted heteroaryl, or two R^(C) groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring; R₄ is hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, —OR^(A), —N(R^(B))₂, —SR^(A), or an oxygen protecting group; m is 0, 1, 2, 3, or 4; R₂ is independently R₂ is hydrogen, optionally substituted C₁₋₆ alkyl, optionally substituted C₂₋₆ alkenyl, optionally substituted C₂₋₆ alkynyl, optionally substituted C₃₋₇ cycloalkyl, optionally substituted 4- to 7-membered heterocyclyl; or optionally substituted C₁₋₄ alkyl-Cy; R₃ is independently hydrogen, C₁₋₄ alkyl, or C₃₋₄ carbocylyl; R_(x) is independently optionally substituted C₁₋₄ alkyl or optionally substituted C₃₋₄ carbocylyl; each instance of R^(A) is independently selected from the group consisting of hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, an oxygen protecting group when attached to an oxygen atom, and a sulfur protecting group when attached to a sulfur atom; each instance of R^(B) is independently selected from the group consisting of hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, and a nitrogen protecting group, or two R^(B) groups are taken together with their intervening atoms to form an optionally substituted heterocyclic ring; and each instance of Cy is independently optionally substituted C₃₋₇ cycloalkyl, optionally substituted 4- to 7-membered heterocyclyl, optionally substituted aryl, optionally substituted heteroaryl; wherein, and unless otherwise specified, heterocyclyl or heterocyclic refers to a radical of a 3-10 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur; carbocyclyl or carbocyclic refers to a radical of a non-aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms and zero heteroatoms in the non-aromatic ring system; aryl refers to a radical of a monocyclic or polycyclic aromatic ring system having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system; and heteroaryl refers to a radical of a 5-10 membered monocyclic or bicyclic 4n+2 aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur.
 2. A compound of claim 1, wherein the compound is of Formula (II):

or a pharmaceutically acceptable salt thereof, wherein: Z is a bond, —O—, —S—, —NR^(B)—, —NR^(B)C(═O)—, —C(═O)NR^(B)—, —OC(═O)NR^(B)—, —NR^(B)C(═O)O—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, trans-CR^(C)═CR^(C)—, cis-CR^(C)═CR^(C)—, —C≡C—, —OC(R^(C))₂—, —C(R^(C))₂O—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(B)—, NR^(B)S(═O)₂—, or an optionally substituted C₁₋₈ hydrocarbon chain, optionally wherein one or more carbon units of the hydrocarbon chain is replaced with —O—, —S—, —NR^(B)—, —NR^(B)C(═O)—, —C(═O)NR^(B)—, —OC(═O)NR^(B)—, —NR^(B)C(═O)O—, —SC(═O)—, —C(═O)S—, —OC(═O)—, —C(═O)O—, —NR^(B)C(═S)—, —C(═S)NR^(B)—, trans-CR^(C)═CR^(C)—, cis-CR^(C)═CR^(C)—, —C≡C—, —OC(R^(C))₂—, —C(R^(C))₂O—, —S(═O)₂O—, —OS(═O)₂—, —S(═O)₂NR^(B)—, —NR^(B)S(═O)₂—, wherein each instance of R^(C) is independently selected from the group consisting of hydrogen, halogen optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, and optionally substituted heteroaryl, or two R^(C) groups are joined to form an optionally substituted carbocyclic or optionally substituted heterocyclic ring; and R₄ is hydrogen, optionally substituted acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, —OR^(A), —N(R^(B))₂, —SR^(A), or an oxygen protecting group.
 3. The compound of claim 2, wherein the compound is of Formula (II-a):

or a pharmaceutically acceptable salt thereof.
 4. The compound of claim 3, wherein R₄ is


5. The compound of claim 3, wherein R₄ is branched C₁₋₁₀ alkyl.
 6. The compound of claim 3, wherein R₄ is

wherein R₅ is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl.
 7. The compound of claim 6, wherein R₄ is


8. The compound of claim 2, wherein the compound is of Formula (II-a1)

or a pharmaceutically acceptable salt thereof, wherein n is 1, 2, 3, 4, 5, 6, 7, or
 8. 9. The compound of claim 2, wherein the compound is of Formula (II-a1-i)

or a pharmaceutically acceptable salt thereof, wherein: each of V₁, V₂, V₃, V₄ and V₅ is independently N or C; R₆ is independently selected from the group consisting of hydrogen, halogen, —N₃, —CN, —NO₂, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted aryl, optionally substituted heterocyclyl, optionally substituted heteroaryl, optionally substituted alkyl-Cy, —OR^(A), —N(R^(B))₂, —SR^(A), —C(═O)R^(A), —C(═O)OR^(A), —C(═O)SR^(A), —C(═O)N(R^(B))₂, —C(═O)N(R^(B))N(R^(B))₂, —OC(═O)R^(A), —OC(═O)N(R^(B))₂, —NR^(B)C(═O)R^(A), —NR^(B)C(═O)N(R^(B))₂, —NR^(B)C(═O)N(R^(B))N(R^(B))₂, —NR^(B)C(═O)OR^(A), —SC(═O)R^(A), —C(═NR^(B))R^(A), —C(═NNR^(B))R^(A), —C(═NOR^(A))R^(A), —C(═NR^(B))N(R^(B))₂, —NR^(B)C(═NR^(B))R^(B), —C(═S)R^(A), —C(═S)N(R^(B))₂, —NR^(B)C(═S)R^(A), —S(═O)R^(A), —OS(═O)₂R^(A), —SO₂R^(A), —NR^(B)SO₂R^(A), or —SO₂N(R^(B))₂; and p is 0, 1, 2, 3, 4, or
 5. 10. The compound of claim 1, wherein the compound is of Formula (II-a1-ii):

or a pharmaceutically acceptable salt thereof.
 11. The compound of claim 1, wherein the compound is of Formula (II-a1-iii):

or a pharmaceutically acceptable salt thereof.
 12. The compound of claim 1, wherein the compound is of Formula (II-a1-iv):

or a pharmaceutically acceptable salt thereof.
 13. The compound of claim 1, wherein the compound is of Formula (II-a1-v):

or a pharmaceutically acceptable salt thereof.
 14. The compound of claim 1, wherein the compound is of Formula (II-a2)

or a pharmaceutically acceptable salt thereof, wherein q is 0, 1, or
 2. 15. The compound of claim 1, wherein the compound is of Formula (II-a3)

or a pharmaceutically acceptable salt thereof.
 16. The compound of claim 1, wherein the compound is of Formula (II-b):

or a pharmaceutically acceptable salt thereof, wherein s is 0, 1, 2, 3, 4, 5, 6, 7, or
 8. 17. The compound of claim 1, wherein the compound is of Formula (II-b1):

or a pharmaceutically acceptable salt thereof.
 18. The compound of claim 1, wherein the compound is of Formula (II-b2):

or a pharmaceutically acceptable salt thereof.
 19. The compound of claim 1, wherein the compound is of Formula (II-b2-i):

or a pharmaceutically acceptable salt thereof.
 20. The compound of claim 1, wherein the compound is of Formula (II-b3):

or a pharmaceutically acceptable salt thereof.
 21. The compound of claim 1, wherein the compound is of Formula (II-c):

or a pharmaceutically acceptable salt thereof, wherein t is 0, 1, 2, 3, 4, 5, 6, 7, or
 8. 22. The compound of claim 1, wherein the compound is of Formula (II-c1):

or a pharmaceutically acceptable salt thereof.
 23. The compound of claim 1, wherein the compound is of Formula (II-c2):

or a pharmaceutically acceptable salt thereof.
 24. The compound of claim 1, wherein the compound is of Formula (II-c2-i):

or a pharmaceutically acceptable salt thereof.
 25. The compound of claim 1, wherein the compound is of Formula (II-c3):

or a pharmaceutically acceptable salt thereof.
 26. The compound of any one of claims 1-25, wherein X is NR₂ and Y is N.
 27. The compound of any one of claims 1-25, wherein X is N and Y is NR₂.
 28. The compound of claim 1, wherein the compound is selected from the group consisting of:


29. A pharmaceutical composition comprising a compound of any one of claims 1-28, or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient.
 30. The pharmaceutical composition of claim 29, wherein the pharmaceutical composition comprises a therapeutically effective amount of the compound.
 31. A kit or packaged pharmaceutical comprising a compound of any one of claims 1-28 or a pharmaceutically acceptable salt thereof, and instructions for use thereof.
 32. A method of inhibiting an arginine methyl tranferase (RMT) comprising contacting a cell with an effective amount of a compound of any one of claims 1-28 or a pharmaceutically acceptable salt thereof.
 33. The method of claim 32, wherein the arginine methyl transferase is PRMT1.
 34. The method of claim 32, wherein the arginine methyl transferase is PRMT3.
 35. The method of claim 32, wherein the arginine methyl transferase is PRMT4.
 36. The method of claim 32, wherein the arginine methyl transferase is PRMT6.
 37. The method of claim 32, wherein the arginine methyl transferase is PRMT8.
 38. A method of modulating gene expression comprising contacting a cell with an effective amount of a compound of any one of claims 1-28 or a pharmaceutically acceptable salt thereof.
 39. A method of modulating transcription comprising contacting a cell with an effective amount of a compound of any one of claims 1-28 or a pharmaceutically acceptable salt thereof.
 40. The method of any one of claims 32-39, wherein the cell is in vitro.
 41. The method of any one of claims 32-39, wherein the cell is in a subject.
 42. A method of treating a RMT-mediated disorder, comprising administering to a subject in need thereof a therapeutically effective amount of a compound of any one of claims 1-28, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition of claim 29 or claim
 30. 43. The method of claim 42, wherein the RMT-mediated disorder is a PRMT1-mediated disorder.
 44. The method of claim 42, wherein the RMT-mediated disorder is a PRMT3-mediated disorder.
 45. The method of claim 42, wherein the RMT-mediated disorder is a PRMT4-mediated disorder.
 46. The method of claim 42, wherein the RMT-mediated disorder is a PRMT6-mediated disorder.
 47. The method of claim 42, wherein the RMT-mediated disorder is a PRMT8-mediated disorder.
 48. The method of claim 42, wherein the disorder is a proliferative disorder.
 49. The method of claim 42, wherein the disorder is cancer. 